qpgraph 2.0.5
Robert Castelo
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/qpgraph | | Last Changed Rev: 97847 / Revision: 102249 | | Last Changed Date: 2014-12-22 06:59:43 -0800 (Mon, 22 Dec 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_2.0.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/qpgraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.0.5’
* 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 ‘qpgraph’ can be installed ... [33s/35s] 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
* 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
eQTLnetworkEstimationParam: no visible global function definition for
‘seqinfo’
show,eQTLnetwork: no visible global function definition for ‘genome’
show,eQTLnetworkEstimationParam: no visible global function definition
for ‘genome’
* 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
File ‘qpgraph/libs/qpgraph.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘reorder.o’
Found ‘srand’, possibly from ‘srand’ (C)
Object: ‘reorder.o’
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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [17s/17s]
[17s/17s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/qpgraph.Rcheck/00check.log’
for details.
* installing *source* package ‘qpgraph’ ...
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Wall -pedantic -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Wall -pedantic -fpic -g -O2 -Wall -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Wall -pedantic -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Wall -pedantic -fpic -g -O2 -Wall -c reorder.c -o reorder.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
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
* DONE (qpgraph)