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BioC 2.12: CHECK report for GlobalAncova on george2

This page was generated on 2013-10-09 09:37:18 -0700 (Wed, 09 Oct 2013).

Package 283/671HostnameOS / ArchBUILDCHECKBUILD BIN
GlobalAncova 3.28.0
Manuela Hummel
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GlobalAncova
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GlobalAncova
Version: 3.28.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GlobalAncova_3.28.0.tar.gz
StartedAt: 2013-10-09 02:12:56 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:16:10 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 194.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GlobalAncova.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GlobalAncova.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GlobalAncova/DESCRIPTION’ ... OK
* this is package ‘GlobalAncova’ version ‘3.28.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GlobalAncova’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... 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
File ‘GlobalAncova/R/zzz.r’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.12-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/libs/GlobalAncova.so’:
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘matrix.o’

Compiled code should not call entry points 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 ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pair.compare 5.073      0   5.152
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/GlobalAncova.Rcheck/00check.log’
for details.

GlobalAncova.Rcheck/00install.out:

* installing *source* package ‘GlobalAncova’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GlobalAncova.c -o GlobalAncova.o
GlobalAncova.c: In function ‘permut_withFperm’:
GlobalAncova.c:186:16: warning: ‘ord_perm’ may be used uninitialized in this function [-Wuninitialized]
GlobalAncova.c: In function ‘permut’:
GlobalAncova.c:289:16: warning: ‘ord_perm’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ludcmp.c -o ludcmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix.c -o matrix.o
gcc -std=gnu99 -shared -L/usr/local/lib -o GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GlobalAncova)

GlobalAncova.Rcheck/GlobalAncova-Ex.timings:

nameusersystemelapsed
GlobalAncova1.8400.0361.879
GlobalAncova.decomp0.7600.0040.767
Plot.all0.1160.0000.113
Plot.genes0.8240.0040.827
Plot.sequential0.0960.0000.092
Plot.subjects1.3040.0081.312
colon.normal0.0120.0040.016
colon.pheno0.0120.0000.012
colon.tumour0.0120.0040.015
genesettesting0.0160.0000.016
pair.compare5.0730.0005.152
pathways0.0080.0040.012
phenodata0.0120.0000.012
vantVeer0.0200.0000.018