Multiple platform build/check report for BioC 3.20 - BUILD results for Rbowtie2 on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 results for Rbowtie2 on palomino8

To the developers/maintainers of the Rbowtie2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie2.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: Rbowtie2

Version: 2.12.0

Command: chmod a+r Rbowtie2 -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Rbowtie2

StartedAt: 2024-12-19 21:22:30 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 21:22:56 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 25.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r Rbowtie2 -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Rbowtie2
###
##############################################################################
##############################################################################


* checking for file 'Rbowtie2/DESCRIPTION' ... OK
* preparing 'Rbowtie2':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/usr/bin/make -f"F:/biocbuild/bbs-3.20-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
F:/biocbuild/bbs-3.20-bioc/R/etc/x64/Makeconf:294: warning: ignoring old recipe for target '.cc.o'
g++ -std=gnu++17  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++17  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++17  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
argparse.cc: In member function 'virtual size_t ar::argparse::knob::consume(ar::string_vec_citer, const ar::string_vec_citer&)':
argparse.cc:481:9: error: 'int64_t' was not declared in this scope
  481 |         int64_t temp = 0;
      |         ^~~~~~~
argparse.cc:39:1: note: 'int64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
   38 | #include "strutils.h"
  +++ |+#include <cstdint>
   39 | 
argparse.cc:483:25: error: 'temp' was not declared in this scope; did you mean 'tm'?
  483 |         if (!(stream >> temp)) {
      |                         ^~~~
      |                         tm
argparse.cc:493:13: error: 'temp' was not declared in this scope; did you mean 'tm'?
  493 |         if (temp >= 0 && temp <= std::numeric_limits<unsigned>::max()) {
      |             ^~~~
      |             tm
make[1]: *** [Makefile.win:46: argparse.o] Error 1
make: *** [Makefile.win:12: all] Error 2
ERROR: compilation failed for package 'Rbowtie2'
* removing 'F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpeUxRvx/Rinst182dc48e445b/Rbowtie2'
      -----------------------------------
ERROR: package installation failed