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BioC 3.1: INSTALL report for biovizBase on zin2

This page was generated on 2015-10-09 09:24:43 -0700 (Fri, 09 Oct 2015).

Package 106/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.16.0
Tengfei Yin
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/biovizBase
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biovizBase
Version: 1.16.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL biovizBase
StartedAt: 2015-10-08 18:12:31 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:12:48 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 16.6 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL biovizBase
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.1-bioc/R/library’
* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
   ^
In file included from /home/biocbuild/bbs-3.1-bioc/R/include/R_ext/RS.h:26:0,
                 from /home/biocbuild/bbs-3.1-bioc/R/include/Rdefines.h:26,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
 extern size_t strlen (const char *__s)
               ^
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
   ^
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
In file included from /home/biocbuild/bbs-3.1-bioc/R/include/R_ext/RS.h:26:0,
                 from /home/biocbuild/bbs-3.1-bioc/R/include/Rdefines.h:26,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:147:12: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
 extern int strncmp (const char *__s1, const char *__s2, size_t __n)
            ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/R/library/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (biovizBase)