Robert Castelo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/qpgraph |
| Branch: RELEASE_3_6 |
| Last Commit: 0442713 |
| Last Changed Date: 2017-10-30 12:39:25 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:19:33 -0400 (Thu, 12 Apr 2018).
| Package 1097/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qpgraph 2.12.0 Robert Castelo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: qpgraph |
| Version: 2.12.0 |
| Command: rm -rf qpgraph.buildbin-libdir qpgraph.Rcheck && mkdir qpgraph.buildbin-libdir qpgraph.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qpgraph.buildbin-libdir qpgraph_2.12.0.tar.gz >qpgraph.Rcheck\00install.out 2>&1 && cp qpgraph.Rcheck\00install.out qpgraph-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=qpgraph.buildbin-libdir --install="check:qpgraph-install.out" --force-multiarch --no-vignettes --timings qpgraph_2.12.0.tar.gz |
| StartedAt: 2018-04-12 02:22:45 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:28:29 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 344.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qpgraph.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf qpgraph.buildbin-libdir qpgraph.Rcheck && mkdir qpgraph.buildbin-libdir qpgraph.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qpgraph.buildbin-libdir qpgraph_2.12.0.tar.gz >qpgraph.Rcheck\00install.out 2>&1 && cp qpgraph.Rcheck\00install.out qpgraph-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=qpgraph.buildbin-libdir --install="check:qpgraph-install.out" --force-multiarch --no-vignettes --timings qpgraph_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/qpgraph.Rcheck' * using R version 3.4.4 (2018-03-15) * 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 '2.12.0' * 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 whether package 'qpgraph' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/HMgmm-class.Rd:65: missing file link 'dspMatrix-class' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/SsdMatrix-class.Rd:14: missing file link 'dspMatrix-class' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/SsdMatrix-class.Rd:27: missing file link 'dspMatrix-class' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/UGgmm-class.Rd:56: missing file link 'dspMatrix-class' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/qpG2Sigma.Rd:51: missing file link 'rmvnorm' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/qpK2ParCor.Rd:17: missing file link 'cov2cor' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/qpgraph.Rcheck/00install.out' for details. * 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 ... OK * 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 shell scripts ... 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/i386/qpgraph.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. 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' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-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
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c cliquer.c -o cliquer.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_fast_path_weight':
qpgraph.c:5849:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
int i = edges[k, 0];
^
qpgraph.c:5850:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
int j = edges[k, 1];
^
qpgraph.c: In function 'ssd_A':
qpgraph.c:8157:17: warning: unused variable 'm' [-Wunused-variable]
int i,j,k,m;
^
qpgraph.c:8157:15: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,m;
^
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:8286:5: warning: assignment from incompatible pointer type
G = LOGICAL(GR);
^
In file included from qpgraph.c:27:0:
qpgraph.c: In function 'qp_fast_edge_nrr':
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:302:13: warning: 'Rf_df' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define pt Rf_pt
^
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:236:13: note: 'Rf_df' was declared here
#define df Rf_df
^
qpgraph.c:5082:16: note: in expansion of macro 'df'
int k, l, df, n_upper_tri;
^
qpgraph.c:5454:11: warning: 'pcorR' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP pcorR;
^
qpgraph.c: In function 'qp_fast_ci_test_hmgm':
qpgraph.c:3976:36: warning: 'rss1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*partial_eta_squared = (rss1 - rss2) / rss0;
^
qpgraph.c:3703:11: note: 'rss1' was declared here
double rss1, rss2;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-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 'det' from package 'Matrix' in package 'qpgraph'
** help
*** installing help indices
converting help for package 'qpgraph'
finding HTML links ... done
EcoliOxygen html
HMgmm-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/HMgmm-class.Rd:65: missing file link 'dspMatrix-class'
SsdMatrix-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/SsdMatrix-class.Rd:14: missing file link 'dspMatrix-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/SsdMatrix-class.Rd:27: missing file link 'dspMatrix-class'
UGgmm-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/UGgmm-class.Rd:56: missing file link 'dspMatrix-class'
eQTLcross-class html
eQTLnetwork-class html
eQTLnetworkEstimate html
eQTLnetworkEstimationParam-class html
graphParam-class html
qpAllCItests html
qpAnyGraph html
qpAvgNrr html
qpBoundary html
qpCItest html
qpClique html
qpCliqueNumber html
qpCov html
qpEdgeNrr html
qpFunctionalCoherence html
qpG2Sigma html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/qpG2Sigma.Rd:51: missing file link 'rmvnorm'
qpGenNrr html
qpGetCliques html
qpGraph-class html
qpGraphDensity html
qpHTF html
qpHist html
qpIPF html
qpImportNrr html
qpK2ParCor html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgPgGey/R.INSTALL374c4c6e3d56/qpgraph/man/qpK2ParCor.Rd:17: missing file link 'cov2cor'
qpNrr html
qpPAC html
qpPCC html
qpPRscoreThreshold html
qpPathWeight html
qpPlotMap html
qpPlotNetwork html
qpPrecisionRecall html
qpRndGraph html
qpRndWishart html
qpTopPairs html
qpUnifRndAssociation html
qpUpdateCliquesRemoving html
qpgraph-package html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'qpgraph' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c cliquer.c -o cliquer.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_fast_path_weight':
qpgraph.c:5849:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
int i = edges[k, 0];
^
qpgraph.c:5850:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
int j = edges[k, 1];
^
qpgraph.c: In function 'ssd_A':
qpgraph.c:8157:17: warning: unused variable 'm' [-Wunused-variable]
int i,j,k,m;
^
qpgraph.c:8157:15: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,m;
^
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:8286:5: warning: assignment from incompatible pointer type
G = LOGICAL(GR);
^
In file included from qpgraph.c:27:0:
qpgraph.c: In function 'qp_edge_nrr':
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:302:13: warning: 'Rf_df' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define pt Rf_pt
^
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:236:13: note: 'Rf_df' was declared here
#define df Rf_df
^
qpgraph.c:5082:16: note: in expansion of macro 'df'
int k, l, df, n_upper_tri;
^
qpgraph.c: In function 'qp_fast_edge_nrr':
qpgraph.c:5454:11: warning: 'pcorR' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP pcorR;
^
qpgraph.c: In function 'qp_ci_test_hmgm.isra.9':
qpgraph.c:3976:36: warning: 'rss1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*partial_eta_squared = (rss1 - rss2) / rss0;
^
qpgraph.c:3703:11: note: 'rss1' was declared here
double rss1, rss2;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qpgraph' as qpgraph_2.12.0.zip
* DONE (qpgraph)
In R CMD INSTALL
In R CMD INSTALL
|
qpgraph.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("qpgraph")
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.
RUNIT TEST PROTOCOL -- Thu Apr 12 02:28:06 2018
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
qpgraph RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.53 0.39 11.92
|
qpgraph.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("qpgraph")
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.
RUNIT TEST PROTOCOL -- Thu Apr 12 02:28:22 2018
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
qpgraph RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
15.56 0.21 15.82
|
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qpgraph.Rcheck/examples_i386/qpgraph-Ex.timings
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qpgraph.Rcheck/examples_x64/qpgraph-Ex.timings
|