Multiple platform build/check report for BioC 3.20 - INSTALL results for seqTools on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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*

INSTALL results for seqTools on palomino4

To the developers/maintainers of the seqTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqTools.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: seqTools

Version: 1.39.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL seqTools

StartedAt: 2024-06-09 15:39:46 -0400 (Sun, 09 Jun 2024)

EndedAt: 2024-06-09 15:40:07 -0400 (Sun, 09 Jun 2024)

EllapsedTime: 21.5 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL seqTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'seqTools' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c seqTools.c -o seqTools.o
seqTools.c: In function 'count_genome_Kmers':
seqTools.c:851:93: warning: format '%u' expects a matching 'unsigned int' argument [-Wformat=]
  851 |                                 error("[count_genome_Kmers] character mismatch at position %u!");
      |                                                                                            ~^
      |                                                                                             |
      |                                                                                             unsigned int
seqTools.c: In function 'scale_kmer_matrix':
seqTools.c:3296:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=]
 3296 |                 error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale);
      |                                                      ~^                             ~~~~~
      |                                                       |                             |
      |                                                       int                           double
      |                                                      %f
seqTools.c:3306:73: warning: format '%i' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=]
 3306 |                                 error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale);
      |                                                                        ~^                             ~~~~~
      |                                                                         |                             |
      |                                                                         int                           double
      |                                                                        %f
gcc -shared -s -static-libgcc -o seqTools.dll tmp.def seqTools.o -lm -LF:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-seqTools/00new/seqTools/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
In fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.21
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (seqTools)