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Package 366/553HostnameOS / ArchBUILDCHECKBUILD BIN
nem 2.32.1
Holger Froehlich
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/nem
Last Changed Rev: 66525 / Revision: 69725
Last Changed Date: 2012-06-08 10:11:11 -0700 (Fri, 08 Jun 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: nem
Version: 2.32.1
Command: rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nem.buildbin-libdir nem_2.32.1.tar.gz >nem-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=nem.buildbin-libdir --install="check:nem-install.out" --force-multiarch --no-vignettes --timings nem_2.32.1.tar.gz && mv nem.buildbin-libdir/* nem.Rcheck/ && rmdir nem.buildbin-libdir
StartedAt: 2012-09-24 01:42:00 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:43:54 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 114.6 seconds
RetCode: 0
Status:  OK  
CheckDir: nem.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/nem.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.32.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'nem' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
get.insertions: warning in transitive.closure(Phinew, mat = TRUE, loop
  = TRUE): partial argument match of 'loop' to 'loops'
moduleNetwork: warning in transitive.closure(modeltotal, mat = TRUE,
  loop = TRUE): partial argument match of 'loop' to 'loops'
nem.calcSignificance : modify.rand: warning in
  transitive.closure(Phinew, mat = TRUE, loop = TRUE): partial argument
  match of 'loop' to 'loops'
sampleRndNetwork: warning in transitive.closure(S, mat = TRUE, loop =
  FALSE): partial argument match of 'loop' to 'loops'
nem: no visible global function definition for 'dynoNEM_MCMC'
nem: no visible global function definition for
  'dynoNEM.posteriorEGenePos'
nem.calcSignificance: no visible binding for global variable
  'inference'
nem.calcSignificance: no visible global function definition for
  'registerDoMC'
nem.calcSignificance: no visible global function definition for
  '%dopar%'
nem.calcSignificance: no visible global function definition for
  'foreach'
nem.featureselection: no visible global function definition for
  'registerDoMC'
nem.featureselection: no visible global function definition for
  '%dopar%'
nem.featureselection: no visible global function definition for
  'foreach'
nem.featureselection: no visible binding for global variable 'd'
nemModelSelection: no visible global function definition for
  'registerDoMC'
nemModelSelection: no visible global function definition for '%dopar%'
nemModelSelection: no visible global function definition for 'foreach'
nemModelSelection: no visible binding for global variable 'lam'
nemModelSelection: no visible binding for global variable 'r'
score: no visible global function definition for 'registerDoMC'
score: no visible global function definition for '%dopar%'
score: no visible global function definition for 'foreach'
score: no visible binding for global variable 'm'
sim.intervention : <anonymous>: no visible global function definition
  for 'dynoNEM.perturb'
* 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.10-bioc/meat/nem.buildbin-libdir/nem/libs/i386/nem.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.10-bioc/meat/nem.buildbin-libdir/nem/libs/x64/nem.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 3 notes.
See
  'E:/biocbld/bbs-2.10-bioc/meat/nem.Rcheck/00check.log'
for details.

nem.Rcheck/00install.out:


install for i386

* installing *source* package 'nem' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=core2 -c MCMC.c -o MCMC.o
MCMC.c: In function 'network_likelihood':
MCMC.c:128:41: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
MCMC.c:137:6: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
MCMC.c: In function 'MCMCrun':
MCMC.c:423:10: warning: unused variable 'stored2' [-Wunused-variable]
MCMC.c:422:10: warning: unused variable 'stored' [-Wunused-variable]
MCMC.c:380:35: warning: unused variable 'mutinf' [-Wunused-variable]
MCMC.c: In function 'network_likelihood':
MCMC.c:160:35: warning: 'loglik0' may be used uninitialized in this function [-Wuninitialized]
MCMC.c: In function 'MCMCrun':
MCMC.c:456:18: warning: 'priorScale_new' may be used uninitialized in this function [-Wuninitialized]
gcc  -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=core2 -c wrapper.c -o wrapper.o
gcc -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o wrapper.o -LE:/biocbld/BBS-2˜1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/nem.buildbin-libdir/nem/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'nem.Rnw' using 'latin1' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'nem' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c MCMC.c -o MCMC.o
MCMC.c: In function 'network_likelihood':
MCMC.c:128:41: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
MCMC.c:137:6: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
MCMC.c: In function 'MCMCrun':
MCMC.c:423:10: warning: unused variable 'stored2' [-Wunused-variable]
MCMC.c:422:10: warning: unused variable 'stored' [-Wunused-variable]
MCMC.c:380:35: warning: unused variable 'mutinf' [-Wunused-variable]
MCMC.c: In function 'network_likelihood':
MCMC.c:156:13: warning: 'loglik0' may be used uninitialized in this function [-Wuninitialized]
MCMC.c: In function 'MCMCrun':
MCMC.c:456:18: warning: 'priorScale_new' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c wrapper.c -o wrapper.o
gcc -m64 -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o wrapper.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/nem.buildbin-libdir/nem/libs/x64
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
* MD5 sums
packaged installation of 'nem' as nem_2.32.1.zip

* DONE (nem)