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This page was generated on 2025-01-11 11:43 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 1435/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.71.0  (landing page)
Benilton Carvalho
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025)
git_url: https://git.bioconductor.org/packages/oligo
git_branch: devel
git_last_commit: b720ab9
git_last_commit_date: 2024-10-29 09:24:49 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

BUILD results for oligo on lconway

To the developers/maintainers of the oligo package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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: oligo
Version: 1.71.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data oligo
StartedAt: 2025-01-10 17:40:05 -0500 (Fri, 10 Jan 2025)
EndedAt: 2025-01-10 17:40:08 -0500 (Fri, 10 Jan 2025)
EllapsedTime: 2.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data oligo
###
##############################################################################
##############################################################################


* checking for file ‘oligo/DESCRIPTION’ ... OK
* preparing ‘oligo’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DABG.c -o DABG.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c:62:11: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  final = Calloc(strlen(result)+1, char);
          ^
ParserGzXYS.c:62:36: error: expected expression
  final = Calloc(strlen(result)+1, char);
                                   ^
ParserGzXYS.c:147:2: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        Free(d0);
        ^
ParserGzXYS.c:147:2: note: did you mean 'free'?
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/malloc/_malloc.h:42:7: note: 'free' declared here
void     free(void *);
         ^
ParserGzXYS.c:153:7: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
      Free(d1); // Missed: 12/02/09
      ^
ParserGzXYS.c:155:3: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  Free(d0);
  ^
5 errors generated.
make: *** [ParserGzXYS.o] Error 1
ERROR: compilation failed for package ‘oligo’
* removing ‘/private/tmp/Rtmp0BxcJF/Rinst13e0d2210517/oligo’
      -----------------------------------
ERROR: package installation failed