Multiple platform build/check report for BioC 3.20 - INSTALL results for Rbowtie2 on palomino6

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4643
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4414
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4442
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4391
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	3833
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 Rbowtie2 on palomino6

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: 2.11.0

Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Rbowtie2

StartedAt: 2024-07-05 15:32:08 -0400 (Fri, 05 Jul 2024)

EndedAt: 2024-07-05 15:32:15 -0400 (Fri, 05 Jul 2024)

EllapsedTime: 6.4 seconds

RetCode: 1

Status: ERROR

Command output

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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Rbowtie2
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.20-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
C:/Users/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 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rbowtie2'