Installation problem of rtracklayer on Bioconductor version 3.19
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Lucille • 0
@e685c3cf
Last seen 9 weeks ago
France

Hi,

I am trying to create a new package to submit to Bioconductor. I am trying to build the package using r-devel (version 4.4). For this I am using the docker image rocker/r-devel. My package vignette uses rtracklayer. When I try to install it on the container I get:

handlers.c: In function 'R_warnHandler':
handlers.c:10:11: error: format not a string literal and no format arguments [-Werror=format-security]

Any idea, how to solve this?

Thank you very much

newpackage rtracklayer • 301 views
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Here is the full output:

> BiocManager::install("rtracklayer")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org/
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-02-18 r85939)
Installing package(s) 'rtracklayer'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/rtracklayer_1.63.0.tar.gz'
Content type 'application/x-gzip' length 4018472 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

* installing *source* package 'rtracklayer' ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: 'gcc (Debian 13.2.0-13) 13.2.0'
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c readGFF.c -o readGFF.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c bbiHelper.c -o bbiHelper.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c bigWig.c -o bigWig.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c bigBedHelper.c -o bigBedHelper.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c bigBed.c -o bigBed.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c chain_io.c -o chain_io.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c twoBit.c -o twoBit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-O3lIg6/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c handlers.c -o handlers.o
handlers.c: In function 'R_warnHandler':
handlers.c:10:11: error: format not a string literal and no format arguments [-Werror=format-security]
   10 |   warning(warn_buf);
      |           ^~~~~~~~
cc1: some warnings being treated as errors
make: *** [/usr/local/lib/R/etc/Makeconf:191: handlers.o] Error 1
ERROR: compilation failed for package 'rtracklayer'
* removing '/usr/local/lib/R/site-library/rtracklayer'

The downloaded source packages are in
    '/tmp/Rtmp4RSBAt/downloaded_packages'
Warning message:
In install.packages(...) :
  installation of package 'rtracklayer' had non-zero exit status
> sessionInfo()
R Under development (unstable) (2024-02-18 r85939)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux bookworm/sid

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so 
LAPACK: /usr/local/lib/R/lib/libRlapack.so;  LAPACK version 3.12.0

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: Etc/UTC
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.4.0      tools_4.4.0        
> BiocManager::version()
[1] '3.19'
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Entering edit mode

Hi Lucille,

Have you looked at the issue here? Consider nudging the developer there as well.

https://github.com/lawremi/rtracklayer/issues/110

To summarize, (for now) use the GH version of rtracklayer with the fix applied:

BiocManager::install("lawremi/rtracklayer")

Best,

Marcel

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Entering edit mode

Thank you so much. I haven't seen it.

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While the maintainer to should fix the code, We've also adjusted the docker image to change the ERROR to a Warning for now. It has just been merged so it should be reflected in an updated docker image shortly

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