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Package 121/553HostnameOS / ArchBUILDCHECKBUILD BIN
CoGAPS 1.6.0
Elana J. Fertig , Michael F. Ochs
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/CoGAPS
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Leopard (10.5.8) / i386 N O T   S U P P O R T E D

Summary

Package: CoGAPS
Version: 1.6.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_1.6.0.tar.gz
StartedAt: 2012-09-24 00:15:19 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:15:47 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 27.5 seconds
RetCode: 0
Status:  OK 
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/CoGAPS.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘1.6.0’
* 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 ‘CoGAPS’ 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 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
calcCoGAPSStat: warning in exists(label, env = results): partial
  argument match of 'env' to 'envir'
calcCoGAPSStat: warning in assign(label, zPerm, env = results): partial
  argument match of 'env' to 'envir'
calcCoGAPSStat: warning in get(label, env = results): partial argument
  match of 'env' to 'envir'
calcCoGAPSStat: warning in assign("GSUpreg", statsUp, env = results):
  partial argument match of 'env' to 'envir'
calcCoGAPSStat: warning in assign("GSDownreg", statsDown, env =
  results): partial argument match of 'env' to 'envir'
calcCoGAPSStat: warning in assign("GSActEst", actEst, env = results):
  partial argument match of 'env' to 'envir'
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘chicago.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* 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-2.10-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.

CoGAPS.Rcheck/00install.out:

* installing *source* package ‘CoGAPS’ ...
checking for prefix by checking for jags... /usr/local/bin/jags
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking Console.h usability... yes
checking Console.h presence... yes
checking for Console.h... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for jags_version in -ljags... yes
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/unix/zzz.R
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include/GAPS-JAGS -I/usr/local/include    -fpic  -g -O2  -Wall -c jags.cc -o jags.o
jags.cc: In function ‘FactoryType asFactoryType(SEXPREC*)’:
jags.cc:320:17: warning: ‘ans’ may be used uninitialized in this function
g++ -shared -L/usr/local/lib64 -o CoGAPS.so jags.o -L/usr/local/lib -ljags -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/CoGAPS.Rcheck/CoGAPS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘CoGAPSUsersManual.Rnw’ 
** testing if installed package can be loaded
module basemod loaded
module gaps loaded

* DONE (CoGAPS)

CoGAPS.Rcheck/CoGAPS-Ex.timings:

nameusersystemelapsed
CoGAPS000
GAPS000