Vince Buffalo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/qrqc |
| Branch: RELEASE_3_9 |
| Last Commit: d6aef92 |
| Last Changed Date: 2019-05-02 11:53:24 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:59:44 -0400 (Wed, 16 Oct 2019).
| Package 1288/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qrqc 1.38.0 Vince Buffalo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | [ OK ] | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: qrqc |
| Version: 1.38.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL qrqc |
| StartedAt: 2019-10-15 19:25:14 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 19:25:56 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 42.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL qrqc
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-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 from incompatible pointer type [-Wincompatible-pointer-types]
#define FILE_OPEN(x, m) (gzopen(x, m))
^
io.c:348:19: note: in expansion of macro ‘FILE_OPEN’
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]
block = kseq_init(fp);
^~
In file included from io.c:12:0:
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
SCOPE kseq_t *kseq_init(type_t fd) \
^
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t) \
^~~~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
block = kseq_init(fp);
^~
In file included from io.c:12:0:
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
SCOPE kseq_t *kseq_init(type_t fd) \
^
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t) \
^~~~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
FILE_CLOSE(fp);
^
io.c:34:32: note: in definition of macro ‘FILE_CLOSE’
#define FILE_CLOSE(x) (gzclose(x))
^
In file included from io.c:31:0:
/usr/include/zlib.h:1631:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
In file included from io.c:12:0:
At top level:
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
SCOPE void kseq_destroy(kseq_t *ks) \
^
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t) \
^~~~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)