Installation issue related to linker files

[ShanSabri]

I'm having issues trying to install Rsamtools via BiocManager::install("Rsamtools").

Error has something to do with linker files, see below:

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Installing package(s) 'Rsamtools'
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Rsamtools_2.14.0.tar.gz'
Content type 'application/x-gzip' length 2873806 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

.Rprofile: Setting R repository:* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
x86_64-conda-linux-gnu-cc -I"/compbio/home/shan.sabri/miniconda3/lib/R/include" -DNDEBUG .Rprofile: Setting R repository:-D_FILE_OFFSET_BITS=64 -I'/compbio/home/shan.sabri/miniconda3/lib/R/library/Rhtslib/include' -I'/compbio/home/shan.sabri/miniconda3/lib/R/library/S4Vectors/include' -I'/compbio/home/shan.sabri/miniconda3/lib/R/library/IRanges/include' -I'/compbio/home/shan.sabri/miniconda3/lib/R/library/XVector/include' -I'/compbio/home/shan.sabri/miniconda3/lib/R/library/Biostrings/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /compbio/home/shan.sabri/miniconda3/include -I/compbio/home/shan.sabri/miniconda3/include -Wl,-rpath-link,/compbio/home/shan.sabri/miniconda3/lib   -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /compbio/home/shan.sabri/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1671440533574/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/compbio/home/shan.sabri/miniconda3=/usr/local/src/conda-prefix  -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-conda-linux-gnu-cc: warning: .Rprofile:: linker input file unused because linking not done
x86_64-conda-linux-gnu-cc: error: .Rprofile:: linker input file not found: No such file or directory
x86_64-conda-linux-gnu-cc: warning: Setting: linker input file unused because linking not done
x86_64-conda-linux-gnu-cc: error: Setting: linker input file not found: No such file or directory
x86_64-conda-linux-gnu-cc: warning: R: linker input file unused because linking not done
x86_64-conda-linux-gnu-cc: error: R: linker input file not found: No such file or directory
x86_64-conda-linux-gnu-cc: warning: repository:-D_FILE_OFFSET_BITS=64: linker input file unused because linking not done
x86_64-conda-linux-gnu-cc: error: repository:-D_FILE_OFFSET_BITS=64: linker input file not found: No such file or directory
make: *** [Biostrings_stubs.o] Error 1
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/compbio/home/shan.sabri/miniconda3/lib/R/library/Rsamtools’

sessionInfo is posted below:

R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /compbio/home/shan.sabri/miniconda3/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.19 compiler_4.2.2      tools_4.2.2
[4] renv_0.16.0

Any help would be greatly appreciated!

[ShanSabri]

SOLVED & closing issue.

The problem was that I had a cat() statement in my ~/.Rprofile that would output ".Rprofile: Setting R repository:" and ended up being pasted into the installation cmd. I simply removed this statement and installation was successful.