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Path mismatch of goTerm2NumberofGenes_Dict.pickle

While running the lines from R_initialize.R, I find the following:

> {
+ use_python(pythonInstanceDir, required = T)
+ py_config()
+ source_python(pythonModuleDir)
+ }
 Error in py_run_file_impl(file, local, convert) : 
FileNotFoundError: [Errno 2] No such file or directory: '/Users/stephen/Dropbox/•LAB DATA/Cm Data/C. merolae Bioinformatics/pipelinepythonscripts/Annotations/goTerm2NumberofGenes_Dict.pickle'

We can look at the traceback:

4.
stop(structure(list(message = "FileNotFoundError: [Errno 2] No such file or directory: '/Users/stephen/Dropbox/•LAB DATA/Cm Data/C. merolae Bioinformatics/pipelinepythonscripts/Annotations/goTerm2NumberofGenes_Dict.pickle'\n", 
call = py_run_file_impl(file, local, convert), cppstack = structure(list(
file = "", line = -1L, stack = c("/home/galen/R/x86_64-pc-linux-gnu-library/4.1/reticulate/libs/reticulate.so(Rcpp::exception::exception(char const*, bool)+0x9a) [0x7f3be4144c8a]", 
"/home/galen/R/x86_64-pc-linux-gnu-library/4.1/reticulate/libs/reticulate.so(Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x29) [0x7f3be41342fa]", ...
3.
py_run_file_impl(file, local, convert)
2.
py_run_file(file, local = FALSE, convert = convert)
1.
source_python(pythonModuleDir)

We can check the following parts:

> getwd()
[1] "/home/galen/Dropbox/UNBC/Rader/RaderLabCode/NewScripts"
> pythonInstanceDir
[1] "/usr/bin/python3"
> pythonModuleDir
[1] "./Deseq2EnrichmentWorkFlowFunctions.py"
> py_config()
python:         /usr/bin/python3
libpython:      /usr/lib/python3.10/config-3.10-x86_64-linux-gnu/libpython3.10.so
pythonhome:     //usr://usr
version:        3.10.6 (main, Aug 10 2022, 11:40:04) [GCC 11.3.0]
numpy:          /usr/lib/python3/dist-packages/numpy
numpy_version:  1.21.5

NOTE: Python version was forced by use_python function

My present understanding is that the line pickle_in = open(os.path.join(annotationDir, "goTerm2NumberofGenes_Dict.pickle"), "rb") in ./Deseq2EnrichmentWorkFlowFunctions.py should be where the path /Users/stephen/Dropbox/•LAB DATA/Cm Data/C. merolae Bioinformatics/pipelinepythonscripts/Annotations/goTerm2NumberofGenes_Dict.pickle comes from. The value of annotationDir in turn comes from annotationDir = global_python_meta.annotationDir in the same file. But I have set annotationDir in global_python_meta to have the correct path to ./Annotations/Annotations. I need to look further into where the incorrect path is coming from.

Au_annotation.csv missing

Running lines from R_initialize.R I get the error:

> coldata <- read.csv(AnnotationFileDirectory, row.names=1)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Au_annotation.csv': No such file or directory

AnnotationFileDirectory is assigned in R_intialize_metadata.R:

AnnotationFileDirectory = "Au_annotation.csv"

I searched the project directory and did not find the file:

RaderLabCode$ find . -type f -iname "Au_annotation.csv"

Do we still need this file?
If we need it, can this be added to a directory such as ./RaderLabCode/Annotations/Annotations?

Pathview is not assigning colours for the equation-by-equation timepoints

This minimum example from the documentation works for multiple columns:

library(pathview)

sim.cpd.data=sim.mol.data(mol.type="cpd", nmol=3000)
sim.cpd.data2 = matrix(sample(sim.cpd.data, 18000,
                              replace = T), ncol = 6)
i <- 3

pv.out <- pathview(gene.data = gse16873.d[, 1:6],
                   pathway.id = "00640",
                   species = "hsa",
                   keys.align = "y",
                   kegg.native = T,
                   match.data = F,
                   multi.state = T,
                   same.layer = T
                   )

This section of code from NewFullRNASeqPipeline.R works for a single condition:

#__________Python Enrichment_________#
percentiles <- c(.99, .95, .90)
test <- keggEnrichmentOnPercentiles(formatedCSVThereshold0, percentiles, metric="score", outputDir=OutputFileDirectory)

pathways <- py_GetAllPathwaysOfSig(test, p_cutoff=1.0)
pathways <- pathways[pathways != 'cme01100' & pathways != 'cme01110'] # Exclude these larger diagrams

keggDataFrame <- py_getKEGGDataframe(formatedCSVThereshold0)

colnames(keggDataFrame)

# kegg_LFC <- keggDataFrame[,c("LFC_LP1hVRM1h", "LFC_LP2hVRM2h", "LFC_LP24hVRM24h", "LFC_LP49hVRM49h")]
scoreFilteredDataFrame = keggDataFrame['Score_LPvRM' >= 33] # 33 comes from LP manuscript; not for general purpose
kegg_LFC <- scoreFilteredDataFrame[,c(paste("LFC_", treated, "v", control, sep="")), drop=FALSE]

#Flip sign so that legend shows green as positive and red negative.
kegg_LFC <- -1*kegg_LFC

#pathview(gene.data = kegg_LFC, pathway.id = "cme03030", species = "cme", gene.idtype = "KEGG",plot.col.key=FALSE)

#kegg_LFC["CYME_CMK133C",]

pv.out.list <- sapply(
  pathways,
  function(pid) pathview(
    gene.data = kegg_LFC,
    pathway.id = pid,
    species = "cme",
    gene.idtype = "KEGG",
    plot.col.key=FALSE
    )
  )

The following approach uses the LPRM data, but the same args as the minimum working example. But it doesn't work. The pathway diagrams are generated, but assigned values are all white.

source("NewFullRNAseqPipeline_metadata.R")

pathways <- scan("../Annotations/Annotations/kegg_pathways.csv", character())
pathways <- pathways[pathways != 'cme01100' & pathways != 'cme01110'] # Exclude these larger diagrams

timepoints <- unique(coldata$timepoint)

t_dfs <- data.frame()
c <- 0
for (t in timepoints) {
  c <- c + 1
  print(t)
  t_col <- coldata[coldata$timepoint == t,]
  t_cts <- cts[grepl(t, colnames(cts))]
  dds <-DESeqDataSetFromMatrix( countData = t_cts,
                                colData = t_col,
                                design = configDesign)
  dds <- DESeq(dds)
  res <- results(dds)
  t_res <- as.data.frame(res)[c("log2FoldChange", "padj")]
  
  t_res$log2FoldChange <- ifelse(t_res$padj < 0.01, t_res$log2FoldChange, 0)
  t_res <- t_res['log2FoldChange']
  names(t_res)[names(t_res) == 'log2FoldChange'] <- paste(t, c, sep='_')
  if (nrow(t_dfs) == 0){
    t_dfs <- t_res
  } else {
    t_dfs = merge(t_dfs, t_res, by="row.names", all=TRUE)
    rownames(t_dfs) <- t_dfs$Row.names
    t_dfs <- subset(t_dfs, select=-c(Row.names))
  }
  }


kegg_LFC <- t_dfs * -1
kegg_LFC <- na.omit(kegg_LFC)
pv.out.list <- sapply(pathways,
                      function(pid) pathview(
                        gene.data = kegg_LFC,
                        pathway.id = pid,
                        species = "cme",
                        gene.idtype = "KEGG",
                        limit = c(min(kegg_LFC), max(kegg_LFC)),
                        keys.align = "y",
                        kegg.native = T,
                        match.data = F,
                        multi.state = T,
                        same.layer = T,
                        plot.col.key=FALSE
                        )
                      )

Why is the coloring graded in the reference?

The coloring of the edges seems to be off. I want to confirm which way the colors should actually be.

Here is a screenshot of one of the reference figures that Stephen sent me:

Here is the current output:

I generated the current output after removing the p-value filter and adding filter for SCORE2 where SCORE2=-log(padj) * (LFC)^2.

I can see that the coloring is similar between the two, however the provided reference figure appears graded by multiple colors. I am not sure why. Maybe multiple genes per box?

Initialization script fails

Within RStudio, I ran the line source("DifferentialExpressionFunctions.R") near the top of R_Initialize.R. The following printout results.


> source("DifferentialExpressionFunctions.R")
Installing packages into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependency ‘FactoMineR’ is not available
also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’, ‘gargle’, ‘curl’, ‘ggpubr’, ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’

trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/pbkrtest_0.5.1.tar.gz'
Content type 'application/x-gzip' length 246327 bytes (240 KB)
==================================================
downloaded 240 KB

trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-30.tar.gz'
Content type 'application/x-gzip' length 3307884 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/car_3.1-0.tar.gz'
Content type 'application/x-gzip' length 569914 bytes (556 KB)
==================================================
downloaded 556 KB

trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.0.tar.gz'
Content type 'application/x-gzip' length 402481 bytes (393 KB)
==================================================
downloaded 393 KB

trying URL 'https://cloud.r-project.org/src/contrib/gargle_1.2.1.tar.gz'
Content type 'application/x-gzip' length 312943 bytes (305 KB)
==================================================
downloaded 305 KB

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
Content type 'application/x-gzip' length 670416 bytes (654 KB)
==================================================
downloaded 654 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggpubr_0.4.0.tar.gz'
Content type 'application/x-gzip' length 2689307 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/googledrive_2.0.0.tar.gz'
Content type 'application/x-gzip' length 1593656 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cloud.r-project.org/src/contrib/googlesheets4_1.0.1.tar.gz'
Content type 'application/x-gzip' length 223314 bytes (218 KB)
==================================================
downloaded 218 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz'
Content type 'application/x-gzip' length 161140 bytes (157 KB)
==================================================
downloaded 157 KB

trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz'
Content type 'application/x-gzip' length 94659 bytes (92 KB)
==================================================
downloaded 92 KB

trying URL 'https://cloud.r-project.org/src/contrib/factoextra_1.0.7.tar.gz'
Content type 'application/x-gzip' length 1386480 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.2.tar.gz'
Content type 'application/x-gzip' length 702514 bytes (686 KB)
==================================================
downloaded 686 KB

* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking for g++ -std=gnu++11 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking for g++ -std=gnu++11 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... no

------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - sudo yum install cmake          (Fedora/CentOS; inside a terminal)
 - sudo apt install cmake          (Debian/Ubuntu; inside a terminal).
 - sudo pacman -S cmake            (Arch Linux; inside a terminal).
 - sudo brew install cmake         (MacOS; inside a terminal with Homebrew)
 - sudo port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------

ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/nloptr’
Warning in install.packages :
  installation of package ‘nloptr’ had non-zero exit status
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/pbkrtest’
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘gargle’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/gargle’
Warning in install.packages :
  installation of package ‘gargle’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘rvest’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/rvest’
Warning in install.packages :
  installation of package ‘rvest’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/googledrive’
Warning in install.packages :
  installation of package ‘googledrive’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/rstatix’
Warning in install.packages :
  installation of package ‘rstatix’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘gargle’, ‘googledrive’, ‘httr’ are not available for package ‘googlesheets4’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/googlesheets4’
Warning in install.packages :
  installation of package ‘googlesheets4’ had non-zero exit status
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/ggpubr’
Warning in install.packages :
  installation of package ‘ggpubr’ had non-zero exit status
ERROR: dependencies ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’ are not available for package ‘tidyverse’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/factoextra’
Warning in install.packages :
  installation of package ‘factoextra’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmpdhd6vt/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29)
Installing package(s) 'DESeq2'
Warning: dependency ‘locfit’ is not available
also installing the dependencies ‘RCurl’, ‘GenomeInfoDb’, ‘annotate’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
Content type 'application/x-gzip' length 731611 bytes (714 KB)
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downloaded 714 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeInfoDb_1.22.1.tar.gz'
Content type 'application/octet-stream' length 3409252 bytes (3.3 MB)
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downloaded 3.3 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz'
Content type 'application/octet-stream' length 1873132 bytes (1.8 MB)
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downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz'
Content type 'application/octet-stream' length 1169872 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/SummarizedExperiment_1.16.1.tar.gz'
Content type 'application/octet-stream' length 1518022 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz'
Content type 'application/octet-stream' length 1421076 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz'
Content type 'application/octet-stream' length 1431450 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz'
Content type 'application/octet-stream' length 2060061 bytes (2.0 MB)
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downloaded 2.0 MB

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’
ERROR: dependency ‘RCurl’ is not available for package ‘annotate’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘locfit’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’

The downloaded source packages are in
	‘/tmp/Rtmpdhd6vt/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
  path: /usr/lib/R/site-library
  packages:
    littler
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29)
Installing package(s) 'DEGreport'
Warning: dependencies ‘lasso2’, ‘locfit’, ‘rjson’ are not available
also installing the dependencies ‘annotate’, ‘RCurl’, ‘GetoptLong’, ‘GenomicRanges’, ‘genefilter’, ‘geneplotter’, ‘GenomeInfoDb’, ‘ComplexHeatmap’, ‘DESeq2’, ‘edgeR’, ‘SummarizedExperiment’

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz'
Content type 'application/octet-stream' length 1873132 bytes (1.8 MB)
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downloaded 1.8 MB

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
Content type 'application/x-gzip' length 731611 bytes (714 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/GetoptLong_1.0.5.tar.gz'
Content type 'application/x-gzip' length 767681 bytes (749 KB)
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trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz'
Content type 'application/octet-stream' length 1169872 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz'
Content type 'application/octet-stream' length 1421076 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz'
Content type 'application/octet-stream' length 1431450 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeInfoDb_1.22.1.tar.gz'
Content type 'application/octet-stream' length 3409252 bytes (3.3 MB)
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downloaded 3.3 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/ComplexHeatmap_2.2.0.tar.gz'
Content type 'application/octet-stream' length 1371868 bytes (1.3 MB)
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downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz'
Content type 'application/octet-stream' length 2060061 bytes (2.0 MB)
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downloaded 2.0 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/edgeR_3.28.1.tar.gz'
Content type 'application/octet-stream' length 1481788 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/SummarizedExperiment_1.16.1.tar.gz'
Content type 'application/octet-stream' length 1518022 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DEGreport_1.22.0.tar.gz'
Content type 'application/octet-stream' length 20151878 bytes (19.2 MB)
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downloaded 19.2 MB

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
ERROR: dependency ‘rjson’ is not available for package ‘GetoptLong’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GetoptLong’
ERROR: dependency ‘locfit’ is not available for package ‘edgeR’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/edgeR’
ERROR: dependency ‘RCurl’ is not available for package ‘annotate’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/annotate’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’
ERROR: dependency ‘GetoptLong’ is not available for package ‘ComplexHeatmap’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/ComplexHeatmap’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘locfit’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’
ERROR: dependencies ‘ComplexHeatmap’, ‘DESeq2’, ‘edgeR’, ‘lasso2’, ‘SummarizedExperiment’ are not available for package ‘DEGreport’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DEGreport’

The downloaded source packages are in
	‘/tmp/Rtmpdhd6vt/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
  path: /usr/lib/R/site-library
  packages:
    littler
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29)
Installing package(s) 'pathview'
also installing the dependencies ‘curl’, ‘RCurl’, ‘httr’, ‘KEGGgraph’, ‘KEGGREST’

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
Content type 'application/x-gzip' length 670416 bytes (654 KB)
==================================================
downloaded 654 KB

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
Content type 'application/x-gzip' length 731611 bytes (714 KB)
==================================================
downloaded 714 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz'
Content type 'application/x-gzip' length 161140 bytes (157 KB)
==================================================
downloaded 157 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/KEGGgraph_1.46.0.tar.gz'
Content type 'application/octet-stream' length 1482115 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/KEGGREST_1.26.1.tar.gz'
Content type 'application/octet-stream' length 25020 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/pathview_1.26.0.tar.gz'
Content type 'application/octet-stream' length 2194351 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/curl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/httr’
ERROR: dependency ‘RCurl’ is not available for package ‘KEGGgraph’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/KEGGgraph’
ERROR: dependency ‘httr’ is not available for package ‘KEGGREST’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/KEGGREST’
ERROR: dependencies ‘KEGGgraph’, ‘KEGGREST’ are not available for package ‘pathview’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/pathview’

The downloaded source packages are in
	‘/tmp/Rtmpdhd6vt/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
  path: /usr/lib/R/site-library
  packages:
    littler
Loading required package: ggplot2

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Error in library(package, character.only = TRUE) : 
  there is no package called ‘factoextra’
In addition: There were 26 warnings (use warnings() to see them)

As explained in the README, certain packages will need to be manually installed.

Au_data.csv missing

Running lines from R_initialize.R I get the error:

> cts <- read.csv(CountFileDirectory, row.names=1)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Au_data.csv': No such file or directory

CountFileDirectory is assigned in R_intialize_metadata.R:

CountFileDirectory = "Au_data.csv"

I searched the project directory and did not find the file:

RaderLabCode$ find . -type f -iname "Au_data.csv"

Do we still need this file?
If we need it, can this be added to a directory such as ./RaderLabCode/Annotations/Annotations?

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