Installation: "Snpcounts.c:82:3: error: ‘for’ loop initial declarations are only allowed in C99 mode"

[kurchejs]

Describe the issue
Hi there, I am attempting to install maftools onto a server-based R studio library, however there seems to be an issue with the gcc options invoked during compilation and the install had non-zero exit status. I attempted to download packages using BiocManager, base install(), and installation from the github repository without success. Any additional ideas are greatly appreciated!

Command
Please post your commands and the output (errors or any unexpected output)

> BiocManager::install("maftools", lib=library)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.25), R 4.3.3 (2024-02-29)
Installing package(s) 'maftools'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/maftools_2.18.0.tar.gz'
Content type 'application/gzip' length 11453947 bytes (10.9 MB)
==================================================
downloaded 10.9 MB

* installing *source* package ‘maftools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)’
gcc -I"/cluster/software/modules-sw/R/4.3.3/lib64/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/cluster/software/modules-sw/R/4.3.3/lib64/R/library/Rhtslib/include' -I'/cluster/software/modules-sw/R/4.3.3/lib64/R/library/zlibbioc/include' -I/usr/local/include    -fpic  -g -O2  -c ntcounts.c -o ntcounts.o
gcc -I"/cluster/software/modules-sw/R/4.3.3/lib64/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/cluster/software/modules-sw/R/4.3.3/lib64/R/library/Rhtslib/include' -I'/cluster/software/modules-sw/R/4.3.3/lib64/R/library/zlibbioc/include' -I/usr/local/include    -fpic  -g -O2  -c snpcounts.c -o snpcounts.o
snpcounts.c: In function ‘snpcounts’:
snpcounts.c:82:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
   for(int i = 0; i < n_contigs; i++){
   ^
snpcounts.c:82:3: note: use option -std=c99 or -std=gnu99 to compile your code
make: *** [snpcounts.o] Error 1
ERROR: compilation failed for package ‘maftools’
* removing ‘/beevol/home/kurchejo/R/x86_64-pc-linux-gnu-library/4.3/maftools’

The downloaded source packages are in
	‘/tmp/RtmpzhaAUq/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘maftools’ had non-zero exit status

Session info
Run sessionInfo() and post the output below

R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /cluster/software/modules-sw/R/4.3.3/lib64/R/lib/libRblas.so 
LAPACK: /cluster/software/modules-sw/R/4.3.3/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

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       

time zone: America/Denver
tzcode source: system (glibc)

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

other attached packages:
[1] dplyr_1.1.4

loaded via a namespace (and not attached):
 [1] desc_1.4.3          utf8_1.2.4          R6_2.5.1           
 [4] tidyselect_1.2.1    magrittr_2.0.3      remotes_2.5.0      
 [7] glue_1.8.0          tibble_3.2.1        pkgconfig_2.0.3    
[10] generics_0.1.3      lifecycle_1.0.4     ps_1.7.6           
[13] cli_3.6.3           processx_3.8.4      fansi_1.0.6        
[16] callr_3.7.6         vctrs_0.6.5         compiler_4.3.3     
[19] rstudioapi_0.16.0   tools_4.3.3         pkgbuild_1.4.4     
[22] curl_5.2.1          pillar_1.9.0        BiocManager_1.30.25
[25] rlang_1.1.4