I am attempting to install Rhtslib on my rstudio pro server via my docker server in which I have several versions of R installed on, working parallel to each other by version in containers. When attempting to install Rhtslib on my working version of R-4.1.1, I get pages of errors. This is triggered by running the standard installation command from an Rsession. The end portion of the long string of errors ends with make errors

I am very aware that this may be caused by my own negligence or error, but I am just looking for anyone who can help point me in the right direction with respect to a resolution. my containers are all running CentOS7 from release 7.6.1810 my set up is vast and I am not able to really list all of the libraries and packages that I have installed but I am happy to provide specific information as it is needed, I can say that I have not had issues installing this with previous versions that I am ware of, and I have Rstudio versions R-3.3.1 - R-4.1.1 and their corresponding bio conductor packages working just fine so far. Any and all help is appreciated, normally at this point I would attempt to install the software into it's own container from source, but with cran packages this is not really a work around I can use and I am not extremely knowledgeable about troubleshooting Rstudio and cran package errors.

Please include input and relevant output here

Once I start an Rsession within my container I run the command to install Rhtslib

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("Rhtslib")

(the output below is not the full output, it is literally pages of output and some of the errors are repeating so in an attempt to make this manageable, I have only grabbed the last main portion of the error message.)

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c:837:9: warning: passing argument 3 of ‘cram_compress_block’ from incompatible pointer type [enabled by default] method, level)) ^

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c:842:6: warning: passing argument 3 of ‘cram_compress_block’ from incompatible pointer type [enabled by default] method, level)) ^

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c:851:8: warning: passing argument 3 of ‘cram_compress_block’ from incompatible pointer type [enabled by default] MIN(9,level))) ^

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c:857:5: warning: passing argument 3 of ‘cram_compress_block’ from incompatible pointer type [enabled by default] method, level)) ^

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c:874:9: warning: passing argument 3 of ‘cram_compress_block’ from incompatible pointer type [enabled by default] method, level)) ^

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c:892:9: warning: passing argument 3 of ‘cram_compress_block’ from incompatible pointer type [enabled by default] methodF, level)) ^

In file included from ./cram/cram.h:59:0, from cram/cram_encode.c:43: /include/htslib/cram.h:326:5: note: expected ‘struct cram_metrics ’ but argument is of type ‘struct cram_metrics ’ int cram_compress_block(cram_fd fd, cram_block b, cram_metrics *metrics, ^

cram/cram_encode.c: In function ‘cram_encode_aux’: cram/cram_encode.c:2245:11: warning: assignment from incompatible pointer type [enabled by default] m->m = k_global ? (cram_metrics *)kh_val(fd->tags_used, k_global) : NULL; ^

make[1]: *** [Makefile.Rhtslib:128: cram/cram_decode.o] Error 1 cram/cram_encode.c: In function ‘cram_put_bam_seq’: cram/cram_encode.c:3167:11: warning: ignoring return value of ‘bam_copy1’, declared with attribute warn_unused_result [-Wunused-result] bam_copy1(c->bams[c->curr_c_rec], b); ^

make[1]: [Makefile.Rhtslib:128: cram/cram_encode.o] Error 1 make[1]: Leaving directory '/tmp/RtmpIzRMxx/R.INSTALL62694832a3/Rhtslib/src/htslib-1.7' make: [Makevars.common:24: htslib] Error 2 ERROR: compilation failed for package ‘Rhtslib’

please also include the results of running the following in an R session

sessionInfo( )

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /n/apps/CentOS7/install/r-4.1.1/lib64/R/lib/libRblas.so LAPACK: /n/apps/CentOS7/install/r-4.1.1/lib64/R/lib/libRlapack.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 utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.1.1

```