Multiple platform build/check report for BioC 3.21 - BUILD BIN results for CGEN on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD BIN results for CGEN on palomino7

To the developers/maintainers of the CGEN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: CGEN

Version: 3.43.0

Command: rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=CGEN.buildbin-libdir CGEN_3.43.0.tar.gz

StartedAt: 2024-12-24 06:49:02 -0500 (Tue, 24 Dec 2024)

EndedAt: 2024-12-24 06:50:01 -0500 (Tue, 24 Dec 2024)

EllapsedTime: 58.9 seconds

RetCode: 0

Status: OK

PackageFile: CGEN_3.43.0.zip

PackageFileSize: 1.753 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=CGEN.buildbin-libdir CGEN_3.43.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'CGEN' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using Fortran compiler: 'GNU Fortran (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:235:25: warning: 't22' may be used uninitialized [-Wmaybe-uninitialized]
  235 |       *g22 = logx - t12 - t22;
      |              ~~~~~~~~~~~^~~~~
Additive.c:207:25: note: 't22' was declared here
  207 |   double t11, t12, t21, t22, x, et11, et12, et21, et22, logx;
      |                         ^~~
Additive.c:233:19: warning: 'et22' may be used uninitialized [-Wmaybe-uninitialized]
  233 |       x    = et12 + et22 - 1;
      |              ~~~~~^~~~~~
Additive.c:207:51: note: 'et22' was declared here
  207 |   double t11, t12, t21, t22, x, et11, et12, et21, et22, logx;
      |                                                   ^~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CML.c -o CML.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ccl.c -o ccl.o
gfortran      -O2  -mfpmath=sse -msse2 -mstackrealign  -c csclust.f -o csclust.o
csclust.f:72:72:

   72 |  10      FLAG(I)=.TRUE.
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fsclust.c -o fsclust.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hcl.c -o hcl.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmatch.c -o pmatch.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c score.c -o score.o
gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/CGEN/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'CGEN' as CGEN_3.43.0.zip
* DONE (CGEN)