Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P [Q] R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for qpgraph on moscato2

This page was generated on 2015-10-09 09:28:26 -0700 (Fri, 09 Oct 2015).

Package 764/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.2.3
Robert Castelo
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/qpgraph
Last Changed Rev: 104779 / Revision: 109384
Last Changed Date: 2015-06-10 07:00:56 -0700 (Wed, 10 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qpgraph
Version: 2.2.3
Command: rm -rf qpgraph.buildbin-libdir qpgraph.Rcheck && mkdir qpgraph.buildbin-libdir qpgraph.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qpgraph.buildbin-libdir qpgraph_2.2.3.tar.gz >qpgraph.Rcheck\00install.out 2>&1 && cp qpgraph.Rcheck\00install.out qpgraph-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=qpgraph.buildbin-libdir --install="check:qpgraph-install.out" --force-multiarch --no-vignettes --timings qpgraph_2.2.3.tar.gz
StartedAt: 2015-10-09 05:09:56 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:16:25 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 389.0 seconds
RetCode: 0
Status:  OK  
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf qpgraph.buildbin-libdir qpgraph.Rcheck && mkdir qpgraph.buildbin-libdir qpgraph.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qpgraph.buildbin-libdir qpgraph_2.2.3.tar.gz >qpgraph.Rcheck\00install.out 2>&1 && cp qpgraph.Rcheck\00install.out qpgraph-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=qpgraph.buildbin-libdir --install="check:qpgraph-install.out" --force-multiarch --no-vignettes --timings qpgraph_2.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/qpgraph.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qpgraph/DESCRIPTION' ... OK
* this is package 'qpgraph' version '2.2.3'
* 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 whether package 'qpgraph' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'GOstats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alleQTL,eQTLnetwork : .local: no visible binding for global variable
  'swappedGenesMarkers'
qpNrr,data.frame : .local: no visible binding for global variable 'm'
reQTLcross,integer-eQTLcross : .local: no visible binding for global
  variable 'n.eQTL'
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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-3.1-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/i386/qpgraph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'E:/biocbld/bbs-3.1-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64/qpgraph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [17s] OK
** running examples for arch 'x64' ... [16s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [16s]
 [17s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [16s]
 [16s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/qpgraph.Rcheck/00check.log'
for details.


qpgraph.Rcheck/00install.out:

install for i386

* installing *source* package 'qpgraph' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cliquer.c -o cliquer.o
cliquer.c: In function 'clique_print_time':
cliquer.c:1802:8: warning: unused variable 'fp' [-Wunused-variable]
cliquer.c: In function 'clique_print_time_always':
cliquer.c:1851:8: warning: unused variable 'fp' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'stat_mis':
qpgraph.c:4247:19: warning: unused variable 'k' [-Wunused-variable]
qpgraph.c:4247:17: warning: unused variable 'j' [-Wunused-variable]
qpgraph.c:4247:15: warning: unused variable 'i' [-Wunused-variable]
qpgraph.c: In function 'lr_em':
qpgraph.c:4289:15: warning: unused variable 'Y_j' [-Wunused-variable]
qpgraph.c:4287:39: warning: variable 'sufStats_ij' set but not used [-Wunused-but-set-variable]
qpgraph.c:4287:27: warning: variable 'sufStats_j' set but not used [-Wunused-but-set-variable]
qpgraph.c:4287:15: warning: variable 'sufStats_i' set but not used [-Wunused-but-set-variable]
qpgraph.c: In function 'ssd_A':
qpgraph.c:8012:17: warning: unused variable 'm' [-Wunused-variable]
qpgraph.c:8012:15: warning: unused variable 'k' [-Wunused-variable]
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:8141:5: warning: assignment from incompatible pointer type [enabled by default]
qpgraph.c: In function 'qp_edge_nrr':
qpgraph.c:5121:67: warning: 'Rf_df' may be used uninitialized in this function [-Wuninitialized]
qpgraph.c: In function 'qp_fast_edge_nrr':
qpgraph.c:5442:11: warning: 'pcorR' may be used uninitialized in this function [-Wuninitialized]
qpgraph.c: In function 'qp_ci_test_hmgm.isra.9':
qpgraph.c:3967:36: warning: 'rss1' may be used uninitialized in this function [-Wuninitialized]
qpgraph.c:3694:11: note: 'rss1' was declared here
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c reorder.c -o reorder.o
gcc -m32 -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lRblas -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'det' from package 'Matrix' in package 'qpgraph'
Creating a generic function from function 'rmvnorm' in package 'qpgraph'
Creating a generic function from function 'sim.cross' in package 'qpgraph'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'qpgraph' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cliquer.c -o cliquer.o
cliquer.c: In function 'clique_print_time':
cliquer.c:1802:8: warning: unused variable 'fp' [-Wunused-variable]
cliquer.c: In function 'clique_print_time_always':
cliquer.c:1851:8: warning: unused variable 'fp' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'stat_mis':
qpgraph.c:4247:19: warning: unused variable 'k' [-Wunused-variable]
qpgraph.c:4247:17: warning: unused variable 'j' [-Wunused-variable]
qpgraph.c:4247:15: warning: unused variable 'i' [-Wunused-variable]
qpgraph.c: In function 'lr_em':
qpgraph.c:4289:15: warning: unused variable 'Y_j' [-Wunused-variable]
qpgraph.c:4287:39: warning: variable 'sufStats_ij' set but not used [-Wunused-but-set-variable]
qpgraph.c:4287:27: warning: variable 'sufStats_j' set but not used [-Wunused-but-set-variable]
qpgraph.c:4287:15: warning: variable 'sufStats_i' set but not used [-Wunused-but-set-variable]
qpgraph.c: In function 'ssd_A':
qpgraph.c:8012:17: warning: unused variable 'm' [-Wunused-variable]
qpgraph.c:8012:15: warning: unused variable 'k' [-Wunused-variable]
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:8141:5: warning: assignment from incompatible pointer type [enabled by default]
qpgraph.c: In function 'qp_edge_nrr':
qpgraph.c:5121:67: warning: 'Rf_df' may be used uninitialized in this function [-Wuninitialized]
qpgraph.c: In function 'qp_fast_edge_nrr':
qpgraph.c:5442:11: warning: 'pcorR' may be used uninitialized in this function [-Wuninitialized]
qpgraph.c: In function 'qp_ci_test_hmgm.isra.9':
qpgraph.c:3967:36: warning: 'rss1' may be used uninitialized in this function [-Wuninitialized]
qpgraph.c:3694:11: note: 'rss1' was declared here
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c reorder.c -o reorder.o
gcc -m64 -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lRlapack -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lRblas -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'qpgraph' as qpgraph_2.2.3.zip
* DONE (qpgraph)

qpgraph.Rcheck/examples_i386/qpgraph-Ex.timings:

nameusersystemelapsed
EcoliOxygen000
qpAllCItests0.180.000.18
qpAnyGraph0.390.000.39
qpAvgNrr2.030.012.05
qpBoundary0.310.000.32
qpCItest0.030.000.03
qpClique0.330.000.32
qpCliqueNumber0.260.000.27
qpCov0.070.000.06
qpEdgeNrr0.020.000.01
qpFunctionalCoherence000
qpG2Sigma0.010.000.02
qpGenNrr0.890.000.89
qpGetCliques0.490.000.48
qpGraphDensity0.350.000.36
qpHTF0.070.020.08
qpHist0.260.000.26
qpIPF0.110.020.13
qpK2ParCor0.030.000.03
qpNrr0.160.000.16
qpPAC0.390.000.40
qpPCC0.060.000.06
qpPRscoreThreshold0.230.000.23
qpPlotMap0.410.010.42
qpPlotNetwork000
qpPrecisionRecall0.230.000.24
qpRndGraph000
qpRndWishart0.020.000.01
qpTopPairs000
qpUnifRndAssociation000
qpUpdateCliquesRemoving0.020.000.02

qpgraph.Rcheck/examples_x64/qpgraph-Ex.timings:

nameusersystemelapsed
EcoliOxygen000
qpAllCItests0.140.000.14
qpAnyGraph0.180.000.19
qpAvgNrr1.830.001.82
qpBoundary0.280.000.28
qpCItest0.030.000.03
qpClique0.670.000.67
qpCliqueNumber0.280.000.28
qpCov0.080.000.08
qpEdgeNrr0.020.000.02
qpFunctionalCoherence0.010.000.01
qpG2Sigma000
qpGenNrr0.550.000.55
qpGetCliques0.320.000.33
qpGraphDensity0.270.020.28
qpHTF0.070.000.38
qpHist0.220.000.22
qpIPF0.110.000.11
qpK2ParCor0.030.000.03
qpNrr0.200.000.21
qpPAC0.450.000.45
qpPCC0.080.000.08
qpPRscoreThreshold0.130.000.12
qpPlotMap0.060.000.06
qpPlotNetwork000
qpPrecisionRecall0.230.000.24
qpRndGraph000
qpRndWishart0.010.000.02
qpTopPairs000
qpUnifRndAssociation000
qpUpdateCliquesRemoving000