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Package 39/479HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpressHTS 1.3.2
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpressHTS
Last Changed Rev: 56536 / Revision: 56603
Last Changed Date: 2011-07-04 02:14:49 -0700 (Mon, 04 Jul 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64 N O T   S U P P O R T E D
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64 N O T   S U P P O R T E D
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64 N O T   S U P P O R T E D
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ArrayExpressHTS
Version: 1.3.2
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpressHTS_1.3.2.tar.gz
StartedAt: 2011-07-06 23:31:33 -0700 (Wed, 06 Jul 2011)
EndedAt: 2011-07-06 23:35:49 -0700 (Wed, 06 Jul 2011)
EllapsedTime: 255.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.3.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘ArrayExpressHTS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cleanupCluster: no visible global function definition for
  ‘cleanupClusters’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

ArrayExpressHTS.Rcheck/00install.out:

* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include"   -fpic  -g -O2 -Wall -c addXS.c -o addXS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include"   -fpic  -g -O2 -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:397:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:397:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:397:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:397:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c: In function ‘fltbam’:
fltbam.c:125:17: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness
/usr/include/string.h:127:14: note: expected ‘char * restrict’ but argument is of type ‘unsigned char *’
fltbam.c:126:17: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:397:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include"   -fpic  -g -O2 -Wall -c functions.c -o functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include"   -fpic  -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include"   -fpic  -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include"   -fpic  -g -O2 -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o -L/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/usrlib/ -lbam -lbcf -ltabix -lz -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
Loading required package: MASS
Loading required package: lpSolve
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘ArrayExpressHTS.Rnw’ 
** testing if installed package can be loaded
Wed Jul  6 23:32:02 2011 [AEHTS] [TRACE] --> initDefaultEnvironment

* DONE (ArrayExpressHTS)

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings:

nameusersystemelapsed
ArrayExpressHTS0.0000.0000.002
ArrayExpressHTSFastQ0.0040.0000.005
getPipelineOption0.0000.0000.001
getPipelineOptions0.0000.0000.001
initDefaultEnvironment0.0000.0000.001
isRCloud0.0000.0000.001
prepareAnnotation0.0000.0000.002
prepareReference0.0000.0000.004
setPipelineOptions000