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My development tidyverse image

Dockerfile 66.53% Shell 9.37% Makefile 24.10%

mytidyverse's Introduction

🐳 𝓡 Custom Tidyverse Docker Image

Installed Dependencies
Build the Image
Changelog

My development tidyverse image is based on r-base.

Installed Dependencies

It adds:

radian as R console replacement
shiny server
- You can start a shiny server using shiny-server.sh
- For details, check the rocker/shiny repo
visidata for the rvisidata package
A whole bunch of libraries for a number of different R packages, mostly for bioinformatics analyses

Build the Image

Run the building process manually using the following code (adapting the version).

docker login
docker build --no-cache -t mytidyverse .
docker tag mytidyverse paulklemm/mytidyverse:4.3.1-3
docker push paulklemm/mytidyverse:4.3.1-3

You can also use the makefile.

make VERSION=4.3.1-3

Changelog

2023-09-15
- Add igraph dependency for scvi
2023-09-11
- Add potential fix for scvi by reverting to pandas < 2.0.0
2023-09-06
- Bump to 4.3.1
- Add scvi tools to interface HypoMap packages
2022-08-03
- Add libgeos-dev dependency required for Seurat
2022-08-02
- Add libncurses5 to comply with Lukas' fibeR package
- Bump to 4.2.1
2022-02-25
- Add anndata and scanpy python modules
- Bump to 4.1.2
2021-09-03
- Fix requirements for magick and tesseract package
2021-08-16
- Add some library to allow ggstatsplot to be installed and bump to 4.1.1
2021-05-26
- Switch to rocker/r-ver as all rocker images >= 4.0.0 are now on Ubuntu 20.04 instead of Debian
2021-02-25
- Bump to 4.0.4
2020-11-30
- Add jags and ibmagick++-dev
2020-10-20
- Clean up Dockerfile and bump to 4.0.3
2020-09-09
- Add required libraries for TFBSTools package
2020-08-27
- Remove RStudio Server
- Switch to rocker/r-ubuntu:20.04
2020-08-25
- Add RStudio Server
2020-07-21
- Bump to r-base:4.0.2
2020-04-17
- Add tmux for rvisidata
2020-04-09
- Bump to r-base:3.6.3
- Remove all R packages
- Add standard shiny installation
2020-02-18
- Bump to r-base:3.6.2
- Add renv
- Add drake
2020-01-13
- Add tidlog
2019-12-13
- Add Visidata not installed properly #4
2019-12-12
- Add hack for fixing issue Fix GenomicAlignments error #3
2019-11-05
- Add visidata 2 pre-release
- Add Fix GenomicAlignments error #3
2019-10-28
- Add styler, knitr, rmarkdown and vroom
2019-10-17
- Add DESeq2
2019-09-02
- Fix broken Uni-Muenster CRAN link
- Update default variables to point to r-base 3.6.1
2019-04-10
- Radix package was renamed to distill
2019-04-05
- Bump base image to r-base:3.5.3
- Add makefile
2019-01-29
- Add Seurat package for Single Cell RNA-Seq analysis
- rtichoke was renamed to radian
2019-01-07
- Switch to r-base:3.5.2 as base image

mytidyverse's People

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mytidyverse's Issues

Fix GenomicAlignments error

Upon installing rmyknife, I encountered a weird error with the GenomicAlignments package. I have no idea what changed, probably it's a good idea to just restart the build in a week.

In file included from /usr/include/stdio.h:867,
                 from /usr/local/lib/R/site-library/Rhtslib/include/sam_opts.c:27,
                 from sam_opts.c:1:
In function ‘fprintf’,
    inlined from ‘parse_sam_global_opt’ at /usr/local/lib/R/site-library/Rhtslib/include/sam_opts.c:85:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:100:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
  100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  101 |    __va_arg_pack ());
      |    ~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_utils.c -o sam_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabixfile.c -o tabixfile.o
tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  190 |     if (bgzf_is_bgzf(fn) != 1)
      |     ^~
In file included from tabixfile.c:3:
/usr/local/lib/R/site-library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
  243 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
      |         ^~~~~~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tagfilter.c -o tagfilter.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/usr/lib/R/bin/R" --vanilla --slave` -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zip_compression.c -o zip_compression.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /usr/local/lib/R/site-library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-Rsamtools/00new/Rsamtools/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 (Rsamtools)
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 -c cigar_utils.c -o cigar_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yxUHwm/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'get_GRangesList_mcols' not found
Error: unable to load R code in package ‘GenomicAlignments’
Execution halted
ERROR: lazy loading failed for package ‘GenomicAlignments’
* removing ‘/usr/local/lib/R/site-library/GenomicAlignments’
Error: Failed to install 'rmyknife' from GitHub:
  (converted from warning) installation of package ‘GenomicAlignments’ had non-zero exit status
Execution halted
The command '/bin/sh -c Rscript -e 'install.packages(c("devtools", "tidyverse", "roxygen2", "ggrepel", "packrat", "usethis", "WriteXLS", "here", "plotly", "svglite", "languageserver", "flexdashboard", "DT", "rJava", "Seurat", "styler", "knitr", "rmarkdown", "vroom"), repos = "http://cloud.r-project.org/"); install.packages("BiocManager", repos = "http://cloud.r-project.org/"); BiocManager::install(c("biomaRt", "clusterProfiler", "DESeq2"), upate=FALSE, ask = FALSE); devtools::install_github("rstudio/distill"); remotes::install_github("yihui/xaringan"); devtools::install_github("paulklemm/mygo"); devtools::install_github("paulklemm/rmyknife"); devtools::install_github("paulklemm/peekr"); devtools::install_github("paulklemm/rvisidata");'' returned a non-zero code: 1

Visidata not installed properly

The visidata preview version is not installed properly.

Traceback (most recent call last):
  File "/usr/local/bin/vd", line 4, in <module>
    __import__('pkg_resources').require('visidata===2.-1dev')
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3250, in <module>
    @_call_aside
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3234, in _call_aside
    f(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3263, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 583, in _build_master
    ws.require(__requires__)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 900, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 786, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'visidata===2.-1dev' distribution was not found and is required by the application

Install radian, not rtichoke

rtichoke changed it's name to radian. Update the installation accordingly.

Add 3.6.1 version

Add support for r-base 3.6.1.

Changes

Apparently the Uni Münster CRAN is offline, so we switched to https://packages.othr.de/cran/
We wanted to add the Visidata v.2 beta, but pip3 threw an error related to accessing the GIT repo when running pip3 install git+git://github.com/saulpw/[email protected]. We have no time for fixing this now, so we're sticking with 1.5.x

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