Zheng Wei
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/Rbowtie2 |
| git_branch: RELEASE_3_19 |
| git_last_commit: f4bb536 |
| git_last_commit_date: 2024-04-30 11:00:12 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | ||||
| Package 1691/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie2 2.10.0 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: Rbowtie2 |
| Version: 2.10.0 |
| Command: chmod a+r Rbowtie2 -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Rbowtie2 |
| StartedAt: 2024-10-16 21:24:16 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 21:24:35 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 18.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### chmod a+r Rbowtie2 -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Rbowtie2
###
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* 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"E:/biocbuild/bbs-3.19-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
E:/biocbuild/bbs-3.19-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 'E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpQJKycq/Rinst4654356125e9/Rbowtie2'
-----------------------------------
ERROR: package installation failed