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This page was generated on 2022-08-12 13:20:41 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 qrqc on nebbiolo1


To the developers/maintainers of the qrqc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qrqc.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 1541/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.50.0  (landing page)
Vince Buffalo
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/qrqc
git_branch: RELEASE_3_15
git_last_commit: e6b52f5
git_last_commit_date: 2022-04-26 11:07:28 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qrqc
Version: 1.50.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL qrqc
StartedAt: 2022-08-11 15:52:44 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 15:53:31 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 47.7 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL qrqc
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_io.c -o R_init_io.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c io.c -o io.o
io.c: In function ‘summarize_file’:
io.c:33:25: warning: initialization of ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
   33 | #define FILE_OPEN(x, m) (gzopen(x, m))
      |                         ^
io.c:348:19: note: in expansion of macro ‘FILE_OPEN’
  348 |   FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
      |                   ^~~~~~~~~
io.c:351:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
  351 |   block = kseq_init(fp);
      |                     ^~
      |                     |
      |                     struct gzFile_s **
In file included from io.c:12:
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:33: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
  170 |  SCOPE kseq_t *kseq_init(type_t fd)         \
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
  241 |  __KSEQ_BASIC(SCOPE, type_t)     \
      |  ^~~~~~~~~~~~
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
  244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
   35 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
  453 |   block = kseq_init(fp);
      |                     ^~
      |                     |
      |                     struct gzFile_s **
In file included from io.c:12:
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:33: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
  170 |  SCOPE kseq_t *kseq_init(type_t fd)         \
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
  241 |  __KSEQ_BASIC(SCOPE, type_t)     \
      |  ^~~~~~~~~~~~
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
  244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
   35 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  454 |   FILE_CLOSE(fp);
      |              ^~
      |              |
      |              struct gzFile_s **
io.c:34:32: note: in definition of macro ‘FILE_CLOSE’
   34 | #define FILE_CLOSE(x) (gzclose(x))
      |                                ^
In file included from /usr/include/zlib.h:34,
                 from io.c:31:
/usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1631 | ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
      |                                ^~
In file included from io.c:12:
At top level:
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
  176 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
  241 |  __KSEQ_BASIC(SCOPE, type_t)     \
      |  ^~~~~~~~~~~~
/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
  244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
   35 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-qrqc/00new/qrqc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qrqc)