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This page was generated on 2023-04-12 11:04:58 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 ArrayExpressHTS on nebbiolo2


To the developers/maintainers of the ArrayExpressHTS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ArrayExpressHTS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 76/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpressHTS 1.48.0  (landing page)
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ArrayExpressHTS
git_branch: RELEASE_3_16
git_last_commit: 3dbd3e8
git_last_commit_date: 2022-11-01 11:05:54 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  ERROR    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.5.1 Monterey / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: ArrayExpressHTS
Version: 1.48.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
StartedAt: 2023-04-10 15:33:36 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 15:33:38 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 1.5 seconds
RetCode: 1
Status:   ERROR  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
   42 |     Rprintf("What?\n");
      |     ^~~~~~~
      |     dprintf
In file included from /usr/include/string.h:495,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:17:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:14:19: note: length computed here
   14 |     int length1 = strlen(text1);
      |                   ^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:18:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:15:19: note: length computed here
   15 |     int length2 = strlen(text2);
      |                   ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fltbam.c -o fltbam.o
fltbam.c:2:10: fatal error: sam.h: No such file or directory
    2 | #include "sam.h"
      |          ^~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.16-bioc/R/etc/Makeconf:169: fltbam.o] Error 1
ERROR: compilation failed for package ‘ArrayExpressHTS’
* removing ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/ArrayExpressHTS’