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Simplify functional enrichment results

Home Page: https://jokergoo.github.io/simplifyEnrichment

License: Other

R 98.14% CSS 1.86%

simplifyenrichment's Introduction

Simplify Functional Enrichment Results

Features

A new method (binary cut) is proposed to efficiently cluster functional terms (e.g. GO terms) into groups from the semantic similarity matrix.
Summaries of functional terms in each cluster are visualized by word clouds.

Citation

Zuguang Gu, et al., simplifyEnrichment: an R/Bioconductor package for Clustering and Visualizing Functional Enrichment Results, Genomics, Proteomics & Bioinformatics 2022. https://doi.org/10.1016/j.gpb.2022.04.008.

Install

simplifyEnrichment is available on Bioconductor, you can install it by:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("simplifyEnrichment")

If you want to try the latest version, install it directly from GitHub:

library(devtools)
install_github("jokergoo/simplifyEnrichment")

Vignette

Usage

As an example, I first generate a list of random GO IDs.

library(simplifyEnrichment)
set.seed(888)
go_id = random_GO(500)
head(go_id)
# [1] "GO:0003283" "GO:0060032" "GO:0031334" "GO:0097476" "GO:1901222"
# [6] "GO:0018216"

Then generate the GO similarity matrix, split GO terms into clusters and visualize it.

mat = GO_similarity(go_id)
simplifyGO(mat)

Examples

License

MIT @ Zuguang Gu

simplifyenrichment's People

Contributors

Stargazers

Watchers

Forkers

jianguozhou3 bioleo chenx-bob duydn msq-123 sulijack xchromosome219 rmflight krassowski joshuamwang j-andrews7 qindan2008 greengilad cateto cailiangliang765 abdo3a

simplifyenrichment's Issues

cluster = 0 for hdbscan

test the runtime for similarity matrices with different size

Implement anno_word_cloud

Error when all cluster size are smaller than the cutoff

mat <-
structure(c(1, 0, 0, 0.5217739479608916, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0.72091597494382831, 0, 0, 0, 0, 1, 0.76570335255640232, 
0, 0.19353711912136234, 0.21294644506436483, 0, 0, 0.16069546596437889, 
0, 0, 0.83230159456882946, 0.15748467589661541, 0.17300013046049459, 
0.1861871274075077, 0.12117670640672897, 0.24422839314131162, 
0, 0.76570335255640232, 1, 0, 0.3777114713465542, 0.40896231651711284, 
0, 0, 0.13011810633393744, 0, 0, 0.68143764566685072, 0.13612980836976893, 
0.14756993670447638, 0.15583744547451689, 0.10101660024243997, 
0.19643920368897208, 0.5217739479608916, 0, 0, 1, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0.69958677444196415, 0, 0, 0, 0, 0.19353711912136234, 
0.3777114713465542, 0, 1, 0.91182904874626591, 0, 0, 0.12359424362384727, 
0, 0, 0.1732580248616688, 0.13119482715892314, 0.22863832856341884, 
0.10664459358133421, 0.096560221096157667, 0.18632537203128252, 
0, 0.21294644506436483, 0.40896231651711284, 0, 0.91182904874626591, 
1, 0, 0, 0.13514258254194136, 0, 0, 0.18865121958013387, 0.13983470217996308, 
0.24499816246339226, 0.11513387705942529, 0.10441067009299211, 
0.20424817672261916, 0, 0, 0, 0, 0, 0, 1, 0.99179154222261412, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.99179154222261412, 
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.16069546596437889, 0.13011810633393744, 
0, 0.12359424362384727, 0.13514258254194136, 0, 0, 1, 0.97838497873844543, 
0, 0.92576303076271849, 0.10175492488458406, 0.1112163635236262, 
0.12477684185218538, 0.1133579858682664, 0.15345538772895337, 
0, 0, 0, 0, 0, 0, 0, 0, 0.97838497873844543, 1, 0, 0.92576303076271849, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.61253207388984798, 
0, 0.75779956970872731, 0, 0, 0, 0.83230159456882946, 0.68143764566685072, 
0, 0.1732580248616688, 0.18865121958013387, 0, 0, 0.92576303076271849, 
0.92576303076271849, 0, 1, 0.14378982296845036, 0.15661428941369931, 
0.16650000873435172, 0.10808083685044109, 0.21279769711632793, 
0, 0.15748467589661541, 0.13612980836976893, 0, 0.13119482715892314, 
0.13983470217996308, 0, 0, 0.10175492488458406, 0, 0.61253207388984798, 
0.14378982296845036, 1, 0.12142366731492545, 0.83266743597444171, 
0.081221862137115172, 0.35854683390219166, 0.72091597494382831, 
0.17300013046049459, 0.14756993670447638, 0.69958677444196415, 
0.22863832856341884, 0.24499816246339226, 0, 0, 0.1112163635236262, 
0, 0, 0.15661428941369931, 0.12142366731492545, 1, 0.097300577088258483, 
0.087947807022519267, 0.16721483615362071, 0, 0.1861871274075077, 
0.15583744547451689, 0, 0.10664459358133421, 0.11513387705942529, 
0, 0, 0.12477684185218538, 0, 0.75779956970872731, 0.16650000873435172, 
0.83266743597444171, 0.097300577088258483, 1, 0.097372229747272457, 
0.44186968764236295, 0, 0.12117670640672897, 0.10101660024243997, 
0, 0.096560221096157667, 0.10441067009299211, 0, 0, 0.1133579858682664, 
0, 0, 0.10808083685044109, 0.081221862137115172, 0.087947807022519267, 
0.097372229747272457, 1, 0.11650843283670112, 0, 0.24422839314131162, 
0.19643920368897208, 0, 0.18632537203128252, 0.20424817672261916, 
0, 0, 0.15345538772895337, 0, 0, 0.21279769711632793, 0.35854683390219166, 
0.16721483615362071, 0.44186968764236295, 0.11650843283670112, 
1), .Dim = c(17L, 17L), .Dimnames = list(c("GO:1990904", "GO:0005739", 
"GO:0005759", "GO:1902494", "GO:0016607", "GO:0016604", "GO:0030055", 
"GO:0005925", "GO:0031967", "GO:0031975", "GO:0098805", "GO:0005740", 
"GO:0035577", "GO:0071013", "GO:0030667", "GO:0005840", "GO:0005794"
), c("GO:1990904", "GO:0005739", "GO:0005759", "GO:1902494", 
"GO:0016607", "GO:0016604", "GO:0030055", "GO:0005925", "GO:0031967", 
"GO:0031975", "GO:0098805", "GO:0005740", "GO:0035577", "GO:0071013", 
"GO:0030667", "GO:0005840", "GO:0005794")), measure = "Rel", ontology = "GO")

Generic simplifyGOFromMultipleLists for gene sets databases other than GO?

Thank you for this great package, I love the word cloud idea, and love the utilities to compare clustering results!

I wonder if it would make sense to create a generic version of simplifyGOFromMultipleLists(), possibly named simplifyEnrichmentFromMultipleLists() to match how simplifyEnrichment() generalises simplifyGO().

Implementation-wise it could be as simple as moving the current function to a non-exported, shared function and allowing to pass a custom callback to it; assuming it would be named simplify_function, it would be:

simplify_function=simplifyGO for simplifyGOFromMultipleLists, and
simplify_function=simplifyEnrichment for simplifyEnrichmentFromMultipleLists

I already solved it for myself by using Heatmap() directly with anno_word_cloud() as an annotation, but this could benefit others.

Implement weighted jaccard/dice...

add a new vignette of how to visualize GO from multiple lists

Expand GO_similarity to work also with GO terms

Hi,

very nice package, congrats!

I wonder whether it would be possible that the function GO_similarity accepts beside GO IDs also GO terms?

E.g. GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION instead of GO:0050434.

I think this feature would brighten the scope of the package a lot as for instance msigdb provides in the download section only the terms and not the IDs.

Thanks,
Christian

ht_clusters(): order of clusters should be adjusted

compare_methods_make_plot uses too many memory

maybe changing the way saving plots?

classification needs to be confirmed by UMAP on the similarity matrix

reorder heatmap

This is awesome!

Just want to leave this here, this is very useful and I'm looking forward to seeing how it develops!

Do not generate the complete dendrogram

check MCL method

it shoud work better.

Can this package be applied to scRNA-seq or scATAC-seq?

This is an awesome package!!! Based on your example, you give a similarity matrix among different GO terms. But I am considering that can this package be applied to scRNA-seq data. For example, If I want to plot a figure that the left panel shows a similarity matrix between cells and the right panel shows some corresponding GO terms or word could of GO terms?

test the stability of binary cut

stop clustering when s < cutoff

We don't need to apply binary cut to the end of every term. It can stop at a node when s < cutoff.

Custom color ramp for simplifyGO() ?

Hi there,
Fantastic work with the package! Is there a way to easily pass a custom color ramp to the simplifyGO() function? E.g. change the heatmap from shades of red to blue.
Best

in supplementary, check the value from Resnik

to check the ranges of the similarity values

compare_similarity(): add pairwise scatterplot

simplifyGO() function doesn't work anymore

I've been using the simplifyGO() function yesterday with 500 terms or so. Today, everything stopped working. I tried to plot with 100x100 matrix, gradually raising the dimensions to 399x399. It worked hastily, the time increasing from 0.1 s to 1.34 secs. When I type in the 499x499 matrix, the following message appears "Cluster 499 terms by 'binary_cut'..." and nothing happens after that. It gets stuck and I'm obliged to stop running the code.
The same happens with the standard example posted on your main page on GitHub.

Test dice coef

order of cl

try running select_cutoff for different datasets

Preserve letter case for selected words in anno_word_cloud

Would it be within the scope of this package to add an argument to anno_word_cloud() which would allow to provide a list of words that should follow a specific letter case pattern? For example the example from README includes "DNA" which should be capitalized, but is lowercase ("dna") in the world cloud:

In a general case I find it difficult to interpret the meaning when seeing gene and protein symbols in an unfamiliar letter case. This is a slight annoyance during interpretation, but also a show stopper for publishing in some journals which might be very strict on gene/protein formatting (so one would need to manually edit the figure, which is best avoided).

In particular this line is enforcing the lowercase formatting and is not user-adjustable:

simplifyEnrichment/R/word_count.R

Lines 27 to 28 in 3dbbaf5

    
           # Convert the text to lower case 
        
           docs = tm_map(docs, content_transformer(tolower))

run select_cutoff()

For each example, also run select_cutoff(), but the figure is not shown in the web page.

partition_by_pam

E-GEOD-13763_A-AFFY-44_g3_g2
E-GEOD-10927_A-AFFY-44_g2_g3

cache argument in binary_cut is not used

Add register method

plot_binary_cut and simplifyGO, the classification/plot is different?

when calculate scores for nodes, remove the values on the diagonal

draw the heatmap without splitting, later lines are aded by decorate...

parallel calculation of GO_similarity()

refer to

https://github.com/jokergoo/epik/blob/master/R/common_utils.R#L162

Error: None of the keys entered are valid keys for 'GOID'

Hi Zuguang,

your new anno_word_cloud_from_GO function is a real help for me. I am trying to annotate a heatmap from a categorical vector with their respective GO terms.

My align_to is just a vector with genes as names:

RF00026'1'
AL669831.1'1'
C1orf159'1'
AL139287.1'1'
CCNL2'1'
AL391244.2'1'

My go_list is a list, where names matches elements in my align_to and their elements are GO terms:

List of 24
$ 7 : chr [1:8] "GO:0006139" "GO:0046483" "GO:0006725" "GO:0016070" ...
$ 2 : chr [1:4] "GO:00160701" "GO:00061391" "GO:00346411" "GO:00464831"
$ 3 : chr [1:2] "GO:0010793" "GO:0034067"
$ 14: chr [1:4] "GO:0006396" "GO:0000959" "GO:0008380" "GO:0002939"
$ 22: chr [1:3] "GO:1990074" "GO:1903690" "GO:1904261"
$ 24: chr [1:7] "GO:0006119" "GO:0046034" "GO:0042775" "GO:0042773" ...
$ 26: chr [1:10] "GO:0001568" "GO:0001944" "GO:0072358" "GO:0072144" ...

The following command does not seem to find my GO terms:

mmy_ha = rowAnnotation(go = anno_word_cloud_from_GO(myalign_to, mygo_id, max_words = 30))

it gives me the following error:

Error in .testForValidKeys(x, keys, keytype, fks): None of the keys entered are valid keys for 'GOID'. Please use the keys method to see a listing of valid arguments.

Any comments?

Best,
Arash

improve it!

ht_cluster(): first page is empty if saved as pdf

compare different clustering results

https://cran.r-project.org/web/packages/ClusterR/index.html
https://cran.r-project.org/web/packages/clusterSim/index.html
https://cran.r-project.org/web/packages/NbClust/index.html

https://cran.r-project.org/web/views/Cluster.html

support more ontologies

DOSE
meshes

Other similarity matrices

BioCor

print more informative message if the format is wrong

#41

How to customize and modify the plot from simplifyGO function?

Thanks for developing such a great package!
I was wondering if the figure coming from simplifyGO is based on ggplot2? Maybe it is based on ComplexHeatmap. I didn't find out the plot object but I would like to modify the figures by myself, like setting the background, theme, title. Any suggestions? Thanks in advance!

Best,
Dongxu

difference score for different partition method

test with more ontologies

tested:

GO BP
DO
KEGG
Reactome

More to test

MsigDB
mixed from multiple ontologies

in compare methods, cluster labels should be adjusted

allows list of GO ids as input

word cloud: consider same words in different forms, ie, nouns, adjectives...

how to get the number of genes in a certain GO

It seems currently it was not so correct.

Installation error

I am having trouble installing simplifyEnrichement on 2 different Mac Computers with different versions of OS and R but no luck. Other R packages seem to install and work okay. I tried installing some packages that gave error manually, but did not work. Could you help me out please? Please see the details and sessionInfo below:

On macOS Catalina with R version 4.0.5

> BiocManager::install("simplyfyEnrichment")
Bioconductor version 3.12 (BiocManager 1.30.12), ?BiocManager::install for help
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31)
Installing package(s) 'simplyfyEnrichment'
Old packages: 'brio', 'cluster', 'later', 'mgcv', 'RSQLite', 'rsvg', 'scatterpie', 'shadowtext', 'V8'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
            binary source needs_compilation
brio         1.1.1  1.1.2              TRUE
later      1.1.0.1  1.2.0              TRUE
RSQLite      2.2.6  2.2.7              TRUE
scatterpie   0.1.5  0.1.6             FALSE
shadowtext   0.0.7  0.0.8             FALSE
V8           3.4.0  3.4.1              TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/cluster_2.1.2.tgz'
Content type 'application/x-gzip' length 605101 bytes (590 KB)
==================================================
downloaded 590 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/mgcv_1.8-35.tgz'
Content type 'application/x-gzip' length 3513655 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rsvg_2.1.1.tgz'
Content type 'application/x-gzip' length 26468777 bytes (25.2 MB)
==================================================
downloaded 25.2 MB


The downloaded binary packages are in
	/var/folders/cv/hxxpfcqj6sqdfcst0z83cw300000gn/T//RtmpBOIiX7/downloaded_packages
installing the source packages ‘brio’, ‘later’, ‘RSQLite’, ‘scatterpie’, ‘shadowtext’, ‘V8’

trying URL 'https://cran.rstudio.com/src/contrib/brio_1.1.2.tar.gz'
Content type 'application/x-gzip' length 12069 bytes (11 KB)
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downloaded 11 KB

trying URL 'https://cran.rstudio.com/src/contrib/later_1.2.0.tar.gz'
Content type 'application/x-gzip' length 64104 bytes (62 KB)
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downloaded 62 KB

trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.2.7.tar.gz'
Content type 'application/x-gzip' length 3616162 bytes (3.4 MB)
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downloaded 3.4 MB

trying URL 'https://cran.rstudio.com/src/contrib/scatterpie_0.1.6.tar.gz'
Content type 'application/x-gzip' length 393045 bytes (383 KB)
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downloaded 383 KB

trying URL 'https://cran.rstudio.com/src/contrib/shadowtext_0.0.8.tar.gz'
Content type 'application/x-gzip' length 188263 bytes (183 KB)
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downloaded 183 KB

trying URL 'https://cran.rstudio.com/src/contrib/V8_3.4.1.tar.gz'
Content type 'application/x-gzip' length 801413 bytes (782 KB)
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downloaded 782 KB

* installing *source* package ‘brio’ ...
** package ‘brio’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c brio.c -o brio.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c file_line_endings.c -o file_line_endings.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_file.c -o read_file.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_file_raw.c -o read_file_raw.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_lines.c -o read_lines.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c write_file.c -o write_file.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c write_lines.c -o write_lines.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o brio.so brio.o file_line_endings.o init.o read_file.o read_file_raw.o read_lines.o write_file.o write_lines.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-brio/00new/brio/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (brio)
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag not needed.
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c callback_registry.cpp -o callback_registry.o
In file included from callback_registry.cpp:6:
In file included from ./callback_registry.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c debug.cpp -o debug.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c later.cpp -o later.o
In file included from later.cpp:1:
In file included from ./later.h:6:
In file included from ./callback_registry.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c later_posix.cpp -o later_posix.o
In file included from later_posix.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
later_posix.cpp:245:13: warning: unused variable 'ret' [-Wunused-variable]
    ssize_t ret = write(dummy_pipe_in, "a", 1);
            ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c later_win32.cpp -o later_win32.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c timer_posix.cpp -o timer_posix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c timestamp_unix.cpp -o timestamp_unix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c timestamp_win32.cpp -o timestamp_win32.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tinycthread.c -o tinycthread.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-later/00new/later/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (later)
* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/plogr/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbColumn.cpp -o DbColumn.o
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:34:
In file included from vendor/boost/container/allocator_traits.hpp:31:
In file included from vendor/boost/container/container_fwd.hpp:63:
vendor/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:25:
vendor/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:27:
vendor/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
4 warnings generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/plogr/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbColumnDataSource.cpp -o DbColumnDataSource.o
In file included from DbColumnDataSource.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from DbColumnDataSource.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:34:
In file included from vendor/boost/container/allocator_traits.hpp:31:
In file included from vendor/boost/container/container_fwd.hpp:63:
vendor/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumnDataSource.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:25:
vendor/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumnDataSource.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:27:
vendor/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
4 warnings generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/plogr/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o
In file included from DbColumnDataSourceFactory.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from DbColumnDataSourceFactory.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:34:
In file included from vendor/boost/container/allocator_traits.hpp:31:
In file included from vendor/boost/container/container_fwd.hpp:63:
vendor/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumnDataSourceFactory.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:25:
vendor/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumnDataSourceFactory.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:27:
vendor/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
4 warnings generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/plogr/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbColumnStorage.cpp -o DbColumnStorage.o
In file included from DbColumnStorage.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from DbColumnStorage.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:34:
In file included from vendor/boost/container/allocator_traits.hpp:31:
In file included from vendor/boost/container/container_fwd.hpp:63:
vendor/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumnStorage.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:25:
vendor/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbColumnStorage.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:27:
vendor/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
4 warnings generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/plogr/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbConnection.cpp -o DbConnection.o
In file included from DbConnection.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from DbConnection.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:34:
In file included from vendor/boost/container/allocator_traits.hpp:31:
In file included from vendor/boost/container/container_fwd.hpp:63:
vendor/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbConnection.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:25:
vendor/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbConnection.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:27:
vendor/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
4 warnings generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/plogr/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbDataFrame.cpp -o DbDataFrame.o
In file included from DbDataFrame.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from DbDataFrame.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:34:
In file included from vendor/boost/container/allocator_traits.hpp:31:
In file included from vendor/boost/container/container_fwd.hpp:63:
vendor/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbDataFrame.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:25:
vendor/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbDataFrame.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from vendor/boost/container/stable_vector.hpp:42:
In file included from vendor/boost/container/detail/allocator_version_traits.hpp:27:
In file included from vendor/boost/container/detail/multiallocation_chain.hpp:28:
In file included from vendor/boost/container/detail/transform_iterator.hpp:28:
In file included from vendor/boost/container/detail/iterator.hpp:24:
In file included from vendor/boost/intrusive/detail/iterator.hpp:27:
vendor/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
vendor/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE {
                                                    ^
In file included from DbDataFrame.cpp:7:
In file included from vendor/boost/bind.hpp:29:
vendor/boost/bind/bind.hpp:1428:10: fatal error: 'boost/bind/bind_template.hpp' file not found
#include <boost/bind/bind_template.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 warnings and 1 error generated.
make: *** [DbDataFrame.o] Error 1
ERROR: compilation failed for package ‘RSQLite’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSQLite’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSQLite’
* installing *source* package ‘scatterpie’ ...
** package ‘scatterpie’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scatterpie)
* installing *source* package ‘shadowtext’ ...
** package ‘shadowtext’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (shadowtext)
* installing *source* package ‘V8’ ...
** package ‘V8’ successfully unpacked and MD5 sums checked
** using staged installation
Found C++14 compiler: clang++ -mmacosx-version-min=10.13
Using CXXCPP=clang++ -mmacosx-version-min=10.13 -std=gnu++14 -E
Using PKG_CFLAGS=-I/usr/local/opt/v8/include -I/usr/local/opt/v8/libexec/include
Using PKG_LIBS=-L/usr/local/opt/v8/libexec -lv8 -lv8_libplatform
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find the libv8 engine library. Try installing:
 * deb: libv8-dev or libnode-dev (Debian / Ubuntu)
 * rpm: v8-devel (Fedora, EPEL)
 * brew: v8 (OSX)
 * csw: libv8_dev (Solaris)
Alternatively, on Linux (x86_64) or MacOS you can set environment variable:
    DOWNLOAD_STATIC_LIBV8=1
to automatically download a static version of libv8.
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
---------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:10: fatal error: 'v8.h' file not found
#include <v8.h>
         ^~~~~~
1 error generated.
------------------------------------------------------------------------
ERROR: configuration failed for package ‘V8’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/V8’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/V8’

The downloaded source packages are in
	‘/private/var/folders/cv/hxxpfcqj6sqdfcst0z83cw300000gn/T/RtmpBOIiX7/downloaded_packages’
Warning messages:
1: package ‘simplyfyEnrichment’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘RSQLite’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘V8’ had non-zero exit status
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.12 compiler_4.0.5      tools_4.0.5         tinytex_0.31        xfun_0.22

On MacOS Catalina with R version 3.6

BiocManager::install("simplyfyEnrichment")
Bioconductor version 3.10 (BiocManager 1.30.12), ?BiocManager::install for help
Bioconductor version '3.10' is out-of-date; the current release version '3.12' is available with R version '4.0'; see
  https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.10 (BiocManager 1.30.12), R 3.6.3 (2020-02-29)
Installing package(s) 'BiocVersion', 'simplyfyEnrichment'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/BiocVersion_3.10.1.tgz'
Content type 'application/x-gzip' length 5574 bytes
==================================================
downloaded 5574 bytes


The downloaded binary packages are in
	/var/folders/cv/hxxpfcqj6sqdfcst0z83cw300000gn/T//RtmpnPFIgX/downloaded_packages
Old packages: 'boot', 'class', 'cluster', 'codetools', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'spatial',
  'survival'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/boot_1.3-27.tgz'
Content type 'application/x-gzip' length 629854 bytes (615 KB)
==================================================
downloaded 615 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/class_7.3-18.tgz'
Content type 'application/x-gzip' length 96154 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/cluster_2.1.2.tgz'
Content type 'application/x-gzip' length 607611 bytes (593 KB)
==================================================
downloaded 593 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/codetools_0.2-18.tgz'
Content type 'application/x-gzip' length 88839 bytes (86 KB)
==================================================
downloaded 86 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/KernSmooth_2.23-18.tgz'
Content type 'application/x-gzip' length 101041 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/lattice_0.20-41.tgz'
Content type 'application/x-gzip' length 1155029 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/MASS_7.3-53.1.tgz'
Content type 'application/x-gzip' length 1168734 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/Matrix_1.3-2.tgz'
Content type 'application/x-gzip' length 4871173 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/mgcv_1.8-35.tgz'
Content type 'application/x-gzip' length 3598092 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/nlme_3.1-152.tgz'
Content type 'application/x-gzip' length 2409422 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/nnet_7.3-15.tgz'
Content type 'application/x-gzip' length 129779 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/spatial_7.3-13.tgz'
Content type 'application/x-gzip' length 158106 bytes (154 KB)
==================================================
downloaded 154 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/survival_3.2-10.tgz'
Content type 'application/x-gzip' length 6807673 bytes (6.5 MB)
==================================================
downloaded 6.5 MB


The downloaded binary packages are in
	/var/folders/cv/hxxpfcqj6sqdfcst0z83cw300000gn/T//RtmpnPFIgX/downloaded_packages
Warning message:
package ‘simplyfyEnrichment’ is not available (for R version 3.6.3) 
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.12 compiler_3.6.3      tools_3.6.3

On MAC OS Mojave with R version 3.6

Bioconductor version 3.10 (BiocManager 1.30.12), ?BiocManager::install for help
Bioconductor version '3.10' is out-of-date; the current release version '3.12' is available with R version '4.0'; see
  https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.10 (BiocManager 1.30.12), R 3.6.3 (2020-02-29)
Installing package(s) 'BiocVersion', 'simplifyEnrichment'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/BiocVersion_3.10.1.tgz'
Content type 'application/x-gzip' length 5574 bytes
==================================================
downloaded 5574 bytes


The downloaded binary packages are in
	/var/folders/kv/5b3zbys92k38jmlb0qbh60hm0000gn/T//RtmpAnJFnA/downloaded_packages
Old packages: 'boot', 'class', 'cluster', 'codetools', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'spatial',
  'survival'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/boot_1.3-27.tgz'
Content type 'application/x-gzip' length 629854 bytes (615 KB)
==================================================
downloaded 615 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/class_7.3-18.tgz'
Content type 'application/x-gzip' length 96154 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/cluster_2.1.2.tgz'
Content type 'application/x-gzip' length 607611 bytes (593 KB)
==================================================
downloaded 593 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/codetools_0.2-18.tgz'
Content type 'application/x-gzip' length 88839 bytes (86 KB)
==================================================
downloaded 86 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/KernSmooth_2.23-18.tgz'
Content type 'application/x-gzip' length 101041 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/lattice_0.20-41.tgz'
Content type 'application/x-gzip' length 1155029 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/MASS_7.3-53.1.tgz'
Content type 'application/x-gzip' length 1168734 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/Matrix_1.3-2.tgz'
Content type 'application/x-gzip' length 4871173 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/mgcv_1.8-35.tgz'
Content type 'application/x-gzip' length 3598092 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/nlme_3.1-152.tgz'
Content type 'application/x-gzip' length 2409422 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/nnet_7.3-15.tgz'
Content type 'application/x-gzip' length 129779 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/spatial_7.3-13.tgz'
Content type 'application/x-gzip' length 158106 bytes (154 KB)
==================================================
downloaded 154 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/survival_3.2-10.tgz'
Content type 'application/x-gzip' length 6807673 bytes (6.5 MB)
==================================================
downloaded 6.5 MB


The downloaded binary packages are in
	/var/folders/kv/5b3zbys92k38jmlb0qbh60hm0000gn/T//RtmpAnJFnA/downloaded_packages
Warning message:
package ‘simplifyEnrichment’ is not available (for R version 3.6.3) 

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.12 compiler_3.6.3      tools_3.6.3

Custom font and background color for word cloud

Hello,
Really great and useful tool. Thanks a lot!
I was trying to change the font color in the word cloud using word_cloud_grob_param

simplifyGO(mat,draw_word_cloud=T,
           word_cloud_grob_param=(col = 1))

Somehow it didn't work and still return the default random color without warning nor error message. I couldn't see which part went wrong. Your insight would be much appreciated.

Also, is it possible to change the background of the word cloud from the default grey scheme?

Thank you again,
Chia-Yi

change anno_link as a right annotation

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