Cannot install oligo on Fedora
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Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 25 minutes ago
Wageningen University, Wageningen, the …

I upgraded my R and Bioconductor installation on my Fedora machine. Upgrading all packages went fine, except for oligo.

The reported errors are rather cryptic to me, so I would appreciate some pointers to fix this.

> BiocManager::install(c('oligo'),force=TRUE)
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Installing package(s) 'oligo'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/oligo_1.68.0.tar.gz'
Content type 'application/x-gzip' length 28421969 bytes (27.1 MB)
==================================================
downloaded 27.1 MB

* installing *source* package 'oligo' ...
** using staged installation
** libs
using C compiler: 'gcc (GCC) 14.1.1 20240507 (Red Hat 14.1.1-1)'
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/preprocessCore/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c DABG.c -o DABG.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/preprocessCore/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function 'gzcountLines':
ParserGzXYS.c:18:17: error: passing argument 1 of 'gzeof' from incompatible pointer type [-Wincompatible-pointer-types]
   18 |   while (!gzeof(file)){
      |                 ^~~~
      |                 |
      |                 struct gzFile_s **
In file included from ParserGzXYS.c:4:
/usr/include/zlib.h:1575:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1575 | Z_EXTERN int Z_EXPORT gzeof(gzFile file);
      |                             ~~~~~~~^~~~
ParserGzXYS.c:19:12: error: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
   19 |     gzgets(file, buffer, 1000);
      |            ^~~~
      |            |
      |            struct gzFile_s **
/usr/include/zlib.h:1472:40: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1472 | Z_EXTERN char * Z_EXPORT gzgets(gzFile file, char *buf, int len);
      |                                 ~~~~~~~^~~~
ParserGzXYS.c: In function 'gzxys_header_field':
ParserGzXYS.c:46:6: error: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types]
   46 |   fp = gzopen(currentFile, "rb");
      |      ^
ParserGzXYS.c:50:10: error: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
   50 |   gzgets(fp, buffer, LINEMAX);
      |          ^~
      |          |
      |          struct gzFile_s **
/usr/include/zlib.h:1472:40: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1472 | Z_EXTERN char * Z_EXPORT gzgets(gzFile file, char *buf, int len);
      |                                 ~~~~~~~^~~~
ParserGzXYS.c:51:11: error: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
   51 |   gzclose(fp);
      |           ^~
      |           |
      |           struct gzFile_s **
/usr/include/zlib.h:1611:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1611 | Z_EXTERN int Z_EXPORT gzclose(gzFile file);
      |                               ~~~~~~~^~~~
ParserGzXYS.c: In function 'R_read_gzxys_files':
ParserGzXYS.c:134:6: error: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types]
  134 |   fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
      |      ^
ParserGzXYS.c:138:11: error: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
  138 |   gzclose(fp);
      |           ^~
      |           |
      |           struct gzFile_s **
/usr/include/zlib.h:1611:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1611 | Z_EXTERN int Z_EXPORT gzclose(gzFile file);
      |                               ~~~~~~~^~~~
make: *** [/usr/lib64/R/etc/Makeconf:195: ParserGzXYS.o] Error 1
ERROR: compilation failed for package 'oligo'
* removing '/usr/lib64/R/library/oligo'
* restoring previous '/usr/lib64/R/library/oligo'

The downloaded source packages are in
        '/tmp/Rtmpv8fwJD/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'oligo'
Update all/some/none? [a/s/n]: n
 Warning message:
In install.packages(...) :
  installation of package 'oligo' had non-zero exit status
> 


> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-redhat-linux-gnu
Running under: Fedora Linux 40 (Forty)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP;  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: Europe/Amsterdam
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] compiler_4.4.0
>
oligo source Install • 1.1k views
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What version of zlib are you running? I can compile with 1.2.7

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Aha, that is a good one!

Starting from release 40, as I just found out, Fedora apparently is not including/using zlib as such anymore, but has changed to zlib-ng. See e.g. here or here.

Compatibility would be maintained through zlib-ng-compat, which would provide zlib 1.2.13.

Currently installed on my machine: zlib-ng-compat-2.1.6-2.fc40. Link.

So it seems oligo is not compatible with zlib 1.2.13?

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There is the zlibbioc package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would require intervention on your part to redirect the makefile to use zlibbioc instead of the system headers.

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Wait a minute. The oligo package is supposed to be using zlibbioc, but apparently it is not. I get the same thing as you do, where it's pointing to the system zlib header instead of zlib.h in the zlibbioc package.

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so whats the solution for this error?

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I think the solution is for the C code in oligo to be updated to work with more modern versions of zlib. The zlibbioc package is really meant to allow Windows users to use zlib, rather than as a header source for *nix based computers (the version of zlib is quite old, and a bunch of the underlying functions are remapped to have bioc_ prepended), so using zlibbioc is just a kludge that is likely suboptimal. It might just be easier to fix the C code instead.

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Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contribute to that.

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FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!

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Thanks James for your continuous attention to this!

Meanwhile Benilton has fixed the zlib problem (thanks for that as well!), and oligo installed fine now.

> packageVersion('oligo')
[1] '1.68.2'
>

For completeness:

> library(oligo)
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-redhat-linux-gnu
Running under: Fedora Linux 40 (Forty)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP;  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: Europe/Amsterdam
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] oligo_1.68.2        Biostrings_2.72.1   GenomeInfoDb_1.40.1
[4] XVector_0.44.0      IRanges_2.38.0      S4Vectors_0.42.0   
[7] Biobase_2.64.0      oligoClasses_1.66.0 BiocGenerics_0.50.0

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0                bit_4.0.5                  
 [3] preprocessCore_1.66.0       jsonlite_1.8.8             
 [5] compiler_4.4.0              BiocManager_1.30.23        
 [7] crayon_1.5.2                SummarizedExperiment_1.34.0
 [9] blob_1.2.4                  affxparser_1.76.0          
[11] GenomicRanges_1.56.0        splines_4.4.0              
[13] fastmap_1.2.0               lattice_0.22-6             
[15] R6_2.5.1                    S4Arrays_1.4.1             
[17] ff_4.0.12                   iterators_1.0.14           
[19] DelayedArray_0.30.1         MatrixGenerics_1.16.0      
[21] GenomeInfoDbData_1.2.12     DBI_1.2.3                  
[23] rlang_1.1.4                 affyio_1.74.0              
[25] cachem_1.1.0                bit64_4.0.5                
[27] memoise_2.0.1               cli_3.6.2                  
[29] RSQLite_2.3.7               SparseArray_1.4.8          
[31] zlibbioc_1.50.0             foreach_1.5.2              
[33] grid_4.4.0                  vctrs_0.6.5                
[35] codetools_0.2-20            abind_1.4-5                
[37] httr_1.4.7                  matrixStats_1.3.0          
[39] tools_4.4.0                 UCSC.utils_1.0.0           
>
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