Error in install.packages("data.table", repos = rep) : unable to install packages

[ebhmayra]

Hello,

I was running deviaTE, and I got the following error. I checked and the library is writable

This was my script:

deviaTE --input_fq vieillardiiBT023_cat_uniq.fq --families ALL --library $data_folder/impolita-families_mcclintok7.fa

This is the error:

During startup - Warning message:
Setting LC_CTYPE failed, using "C"
Warning in install.packages("data.table", repos = rep) :
'lib = "/home/apps/conda/miniconda3/envs/devia-te-0.3.8/lib/R/library"' is not writable
Error in install.packages("data.table", repos = rep) :
unable to install packages
Execution halted

End of deviaTE run

Best wishes,
Mayra

[W-L]

Hi Mayra,
I'm afraid I can't reproduce the issue. The packages are installing fine for me on a new conda environment. Would you mind running ls -l /home/apps/conda/miniconda3/envs/devia-te-0.3.8/lib/R/library and posting the output? Just to double-check that the directory exists and is writable by your user.

[ebhmayra]

Hi,

Here the output:
....
total 812
drwxrwxr-x 10 appadmin appadmin 15 May 8 14:00 MASS
drwxrwxr-x 12 appadmin appadmin 22 May 8 14:00 Matrix
drwxrwxr-x 7 appadmin appadmin 12 May 8 14:00 R6
drwxrwxr-x 6 appadmin appadmin 10 May 8 14:00 RColorBrewer
drwxrwxr-x 16 appadmin appadmin 23 May 8 14:00 Rcpp
drwxrwxr-x 8 appadmin appadmin 13 May 8 14:00 argparse
drwxrwxr-x 6 appadmin appadmin 9 May 8 14:00 assertthat
drwxrwxr-x 7 appadmin appadmin 10 May 8 14:00 base
drwxrwxr-x 6 appadmin appadmin 11 May 8 14:00 cli
drwxrwxr-x 10 appadmin appadmin 16 May 8 14:00 colorspace
drwxrwxr-x 6 appadmin appadmin 9 May 8 14:00 compiler
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 cowplot
drwxrwxr-x 6 appadmin appadmin 16 May 8 14:00 crayon
drwxrwxr-x 9 appadmin appadmin 14 May 8 14:00 data.table
drwxrwxr-x 6 appadmin appadmin 9 May 8 14:00 datasets
drwxrwxr-x 7 appadmin appadmin 10 May 8 14:00 dichromat
drwxrwxr-x 9 appadmin appadmin 13 May 8 14:00 digest
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 fansi
drwxrwxr-x 6 appadmin appadmin 11 May 8 14:00 findpython
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 getopt
drwxrwxr-x 8 appadmin appadmin 14 May 8 14:00 ggplot2
drwxrwxr-x 8 appadmin appadmin 13 May 8 14:00 glue
drwxrwxr-x 11 appadmin appadmin 14 May 8 14:00 grDevices
drwxrwxr-x 8 appadmin appadmin 11 May 8 14:00 graphics
drwxrwxr-x 8 appadmin appadmin 11 May 8 14:00 grid
drwxrwxr-x 8 appadmin appadmin 12 May 8 14:00 gridExtra
drwxrwxr-x 6 appadmin appadmin 10 May 8 14:00 gtable
drwxrwxr-x 8 appadmin appadmin 14 May 8 14:00 jsonlite
drwxrwxr-x 6 appadmin appadmin 10 May 8 14:00 labeling
drwxrwxr-x 10 appadmin appadmin 15 May 8 14:00 lattice
drwxrwxr-x 8 appadmin appadmin 12 May 8 14:00 lazyeval
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 magrittr
drwxrwxr-x 7 appadmin appadmin 10 May 8 14:00 methods
drwxrwxr-x 9 appadmin appadmin 13 May 8 14:00 mgcv
drwxrwxr-x 7 appadmin appadmin 12 May 8 14:00 munsell
drwxrwxr-x 11 appadmin appadmin 16 May 8 14:00 nlme
drwxrwxr-x 8 appadmin appadmin 11 May 8 14:00 parallel
drwxrwxr-x 6 appadmin appadmin 10 May 8 14:00 pillar
drwxrwxr-x 8 appadmin appadmin 13 May 8 14:00 plyr
drwxrwxr-x 8 appadmin appadmin 16 May 8 14:00 proto
drwxrwxr-x 8 appadmin appadmin 14 May 8 14:00 reshape2
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 rlang
drwxrwxr-x 7 appadmin appadmin 12 May 8 14:00 scales
drwxrwxr-x 7 appadmin appadmin 10 May 8 14:00 splines
drwxrwxr-x 8 appadmin appadmin 13 May 8 14:00 stats
drwxrwxr-x 6 appadmin appadmin 9 May 8 14:00 stats4
drwxrwxr-x 8 appadmin appadmin 15 May 8 14:00 stringi
drwxrwxr-x 9 appadmin appadmin 14 May 8 14:00 stringr
drwxrwxr-x 9 appadmin appadmin 12 May 8 14:00 tcltk
drwxrwxr-x 8 appadmin appadmin 13 May 8 14:00 tibble
drwxrwxr-x 7 appadmin appadmin 10 May 8 14:00 tools
drwxrwxr-x 20 appadmin appadmin 21 May 8 14:00 translations
drwxrwxr-x 8 appadmin appadmin 13 May 8 14:00 utf8
drwxrwxr-x 10 appadmin appadmin 14 May 8 14:00 utils
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 viridisLite
drwxrwxr-x 7 appadmin appadmin 11 May 8 14:00 withr

...

Best,
Mayra

[W-L]

Thanks! Is this a shared system, or is appadmin your user? Any other user trying to write in this directory would probably get an error about the directory being not writable (3rd permission indicator r-x). Or in other words, was the conda environment created by the same user as running the command in your original post?

[ebhmayra]

Hi,

Yes, this is a computer cluster, so devia-Te was installed there by the central administrator. I just checked that all programs installed there have the r-x, not writable permission for everyone (third permission).

Best,
Mayra

[W-L]

I see. This tool was created when R integration in conda was a bit patchy and not all packages were available, so installation of R packages was done during the first execution of the program instead. This is definitely not ideal, especially when users don't have the permission to do that like in your case. There are two options you can try: i) either installation with one of the other methods described in the readme, if any of them work with your user permissions. ii) Use a more complete conda specification that also includes the R packages. For this, you could ask your admin to install from this yaml specification instead (just exported this from a fresh working installation on my system):

name: deviaTE_env
channels:
  - w-l
  - r
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - _r-mutex=1.0.0=anacondar_1
  - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
  - bcftools=1.9=h47928c2_2
  - binutils_impl_linux-64=2.35.1=h27ae35d_9
  - binutils_linux-64=2.35.1=h454624a_30
  - blas=1.0=openblas
  - bwa=0.7.17=h5bf99c6_8
  - bwidget=1.9.11=1
  - bzip2=1.0.8=h7b6447c_0
  - ca-certificates=2023.01.10=h06a4308_0
  - cairo=1.14.12=h8948797_3
  - certifi=2021.5.30=py36h06a4308_0
  - curl=7.61.1=hbc83047_0
  - deviate=0.3.8=py36_0
  - expat=2.4.9=h6a678d5_0
  - fontconfig=2.14.1=h52c9d5c_1
  - freetype=2.12.1=h4a9f257_0
  - fribidi=1.0.10=h7b6447c_0
  - gcc_impl_linux-64=7.5.0=h7105cf2_17
  - gcc_linux-64=7.5.0=h8f34230_30
  - gdbm=1.18=h941a26a_0
  - gfortran_impl_linux-64=7.5.0=ha8c8e06_17
  - gfortran_linux-64=7.5.0=h96bb648_30
  - glib=2.56.2=hd408876_0
  - graphite2=1.3.14=h295c915_1
  - gsl=2.4=h14c3975_4
  - gxx_impl_linux-64=7.5.0=h0a5bf11_17
  - gxx_linux-64=7.5.0=hffc177d_30
  - harfbuzz=1.8.8=hffaf4a1_0
  - htslib=1.9=h47928c2_5
  - icu=58.2=he6710b0_3
  - jpeg=9e=h5eee18b_1
  - kernel-headers_linux-64=3.10.0=h57e8cba_10
  - krb5=1.16.4=h173b8e3_0
  - ld_impl_linux-64=2.35.1=h7274673_9
  - libcurl=7.61.1=h20c2e04_0
  - libdeflate=1.0=h14c3975_1
  - libedit=3.1.20181209=hc058e9b_0
  - libffi=3.2.1=hf484d3e_1007
  - libgcc-devel_linux-64=7.5.0=hbbeae57_17
  - libgcc-ng=11.2.0=h1234567_1
  - libgfortran-ng=7.5.0=ha8ba4b0_17
  - libgfortran4=7.5.0=ha8ba4b0_17
  - libgomp=11.2.0=h1234567_1
  - libopenblas=0.3.18=hf726d26_0
  - libpng=1.6.39=h5eee18b_0
  - libssh2=1.10.0=h8f2d780_0
  - libstdcxx-devel_linux-64=7.5.0=hf0c5c8d_17
  - libstdcxx-ng=11.2.0=h1234567_1
  - libtiff=4.2.0=hecacb30_2
  - libuuid=1.41.5=h5eee18b_0
  - libwebp-base=1.2.4=h5eee18b_1
  - libxcb=1.15=h7f8727e_0
  - libxml2=2.9.14=h74e7548_0
  - lz4-c=1.9.4=h6a678d5_0
  - make=4.2.1=h1bed415_1
  - ncurses=6.1=he6710b0_1
  - numpy=1.17.0=py36h99e49ec_0
  - numpy-base=1.17.0=py36h2f8d375_0
  - openssl=1.1.1t=h7f8727e_0
  - pandas=0.23.4=py36h04863e7_0
  - pango=1.42.4=h049681c_0
  - pcre=8.45=h295c915_0
  - perl=5.34.0=h5eee18b_2
  - pip=21.2.2=py36h06a4308_0
  - pixman=0.40.0=h7f8727e_1
  - pysam=0.15.1=py36h0380709_0
  - python=3.6.10=h0371630_0
  - python-dateutil=2.8.2=pyhd3eb1b0_0
  - pytz=2021.3=pyhd3eb1b0_0
  - r-argparse=1.1.1=r351h6115d3f_0
  - r-assertthat=0.2.0=r351h6115d3f_0
  - r-base=3.5.1=h1e0a451_2
  - r-cli=1.0.0=r351h6115d3f_1
  - r-colorspace=1.3_2=r351h96ca727_0
  - r-cowplot=0.9.3=r351h6115d3f_1001
  - r-crayon=1.3.4=r351h6115d3f_0
  - r-data.table=1.11.6=r351hc070d10_0
  - r-dichromat=2.0_0=r351h6115d3f_4
  - r-digest=0.6.15=r351h96ca727_0
  - r-fansi=0.2.3=r351h96ca727_0
  - r-findpython=1.0.3=r351h6115d3f_0
  - r-getopt=1.20.2=r351h6115d3f_0
  - r-ggplot2=3.0.0=r351h6115d3f_0
  - r-glue=1.3.0=r351h96ca727_0
  - r-gridextra=2.3=r351h6115d3f_0
  - r-gtable=0.2.0=r351h6115d3f_0
  - r-jsonlite=1.5=r351h96ca727_0
  - r-labeling=0.3=r351h6115d3f_4
  - r-lattice=0.20_35=r351h96ca727_0
  - r-lazyeval=0.2.1=r351h96ca727_0
  - r-magrittr=1.5=r351h6115d3f_4
  - r-mass=7.3_50=r351h96ca727_0
  - r-matrix=1.2_14=r351h96ca727_0
  - r-mgcv=1.8_24=r351h96ca727_0
  - r-munsell=0.5.0=r351h6115d3f_0
  - r-nlme=3.1_137=r351ha65eedd_0
  - r-pillar=1.3.0=r351h6115d3f_0
  - r-plyr=1.8.4=r351h29659fb_0
  - r-proto=1.0.0=r351h6115d3f_0
  - r-r6=2.2.2=r351h6115d3f_0
  - r-rcolorbrewer=1.1_2=r351h6115d3f_0
  - r-rcpp=0.12.18=r351h29659fb_0
  - r-reshape2=1.4.3=r351h29659fb_0
  - r-rlang=0.2.1=r351h96ca727_0
  - r-scales=0.5.0=r351h29659fb_0
  - r-stringi=1.2.4=r351h29659fb_0
  - r-stringr=1.3.1=r351h6115d3f_0
  - r-tibble=1.4.2=r351h96ca727_0
  - r-utf8=1.1.4=r351h96ca727_0
  - r-viridislite=0.3.0=r351h6115d3f_0
  - r-withr=2.1.2=r351h6115d3f_0
  - readline=7.0=h7b6447c_5
  - samtools=1.9=h8ee4bcc_1
  - setuptools=58.0.4=py36h06a4308_0
  - six=1.16.0=pyhd3eb1b0_1
  - sqlite=3.31.1=h7b6447c_0
  - sysroot_linux-64=2.17=h57e8cba_10
  - tk=8.6.12=h1ccaba5_0
  - tktable=2.10=h14c3975_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - xz=5.2.10=h5eee18b_1
  - zlib=1.2.13=h5eee18b_0
  - zstd=1.5.5=hc292b87_0

Apologies for the hassle, and please let me know if this works out. Once I have some more time, I'll improve the installation procedure to avoid this.

[ebhmayra]

Hi,

I installed it locally (on my user account), and it works, but I got another error:

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

However, I solved it by loading Samtools before activating deviaTE_env

So, thank you very much for your help.

Best,
Mayra

[W-L]

Thanks very much for reporting back, and glad that it worked out this way. The error about shared libraries of samtools is an issue on their end with some dependencies of that specific version. It can be solved by creating a link to the library (replacing the correct path to the library folder of your conda env if different to this example):

cd ~/miniconda3/envs/deviaTE_env/lib/
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0

I'll make sure to update the dependencies to a newer version of samtools to avoid this, so will leave the issue open until then.
Thanks again