ArrayExpressHTS 1.8.0
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
addOptions: warning in assign(names[i], new[[i]], env = options):
partial argument match of 'env' to 'envir'
addPackageVariables: warning in assign(names[i], new[[i]], env =
variables): partial argument match of 'env' to 'envir'
createOptions: warning in assign(names[i], new[[i]], env = options):
partial argument match of 'env' to 'envir'
getPackageVariable: warning in get(name, env = variables): partial
argument match of 'env' to 'envir'
getPipelineOption: warning in get(name, env = options): partial
argument match of 'env' to 'envir'
myHTMLplot: warning in assign(".HTML.graph", TRUE, env = get("HTMLenv",
envir = .GlobalEnv)): partial argument match of 'env' to 'envir'
setPackageVariable: warning in assign(names[i], list[[i]], env =
defaultVariables): partial argument match of 'env' to 'envir'
setPipelineOption: warning in assign(name, value, env =
defaultOptions): partial argument match of 'env' to 'envir'
cleanupCluster: no visible global function definition for
‘cleanupClusters’
prepareCluster: no visible global function definition for
‘mergeClusters’
* 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
Found ‘printf’, possibly from ‘printf’ (C)
Objects: ‘addXS.o’, ‘fltbam.o’, ‘functions.o’
Found ‘putchar’, possibly from ‘putchar’ (C)
Object: ‘fltbam.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘addXS.o’, ‘fltbam.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘fltbam.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Object: ‘fltbam.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... 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
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c addXS.c -o addXS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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 [-Wpointer-sign]
/usr/include/string.h:399:15: 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 [-Wpointer-sign]
/usr/include/string.h:399:15: 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 [-Wpointer-sign]
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 [-Wpointer-sign]
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 [-Wpointer-sign]
/usr/include/string.h:399:15: 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 [-Wpointer-sign]
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 [-Wpointer-sign]
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 [-Wpointer-sign]
/usr/include/string.h:399:15: 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 [-Wpointer-sign]
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 [-Wpointer-sign]
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 [-Wpointer-sign]
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 [-Wpointer-sign]
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 [-Wpointer-sign]
/usr/include/string.h:128:14: 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 [-Wpointer-sign]
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:96:21: warning: variable ‘kk’ set but not used [-Wunused-but-set-variable]
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined [enabled by default]
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined [enabled by default]
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined [enabled by default]
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c functions.c -o functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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 /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘ArrayExpressHTS.Rnw’
** testing if installed package can be loaded
Sun Mar 24 23:20:36 2013 [AEHTS] Setting Options Step 1
Sun Mar 24 23:20:36 2013 [AEHTS] Setting Options Step 2
Sun Mar 24 23:20:36 2013 [AEHTS] Setting Options Step 3
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] fasta_formatter not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] cufflinks not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] samtools not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] bwa not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] mmseq not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] bam2hits not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] bowtie not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] *** WARNING ***
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] tophat not found
Sun Mar 24 23:20:36 2013 [AEHTS]
Sun Mar 24 23:20:36 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Sun Mar 24 23:20:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 23:20:36 2013 [AEHTS]
* DONE (ArrayExpressHTS)