BioC 3.5: CHECK report for groHMM on tokay2
This page was generated on 2017-08-16 13:23:54 -0400 (Wed, 16 Aug 2017).
groHMM 1.10.0
Anusha Nagari , Venkat Malladi , Tulip Nandu , W. Lee Kraus
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/groHMM | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: groHMM
|
| Version: 1.10.0
|
| Command: rm -rf groHMM.buildbin-libdir groHMM.Rcheck && mkdir groHMM.buildbin-libdir groHMM.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=groHMM.buildbin-libdir groHMM_1.10.0.tar.gz >groHMM.Rcheck\00install.out 2>&1 && cp groHMM.Rcheck\00install.out groHMM-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=groHMM.buildbin-libdir --install="check:groHMM-install.out" --force-multiarch --no-vignettes --timings groHMM_1.10.0.tar.gz
|
| StartedAt: 2017-08-16 00:20:33 -0400 (Wed, 16 Aug 2017)
|
| EndedAt: 2017-08-16 00:25:15 -0400 (Wed, 16 Aug 2017)
|
| EllapsedTime: 282.8 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: groHMM.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf groHMM.buildbin-libdir groHMM.Rcheck && mkdir groHMM.buildbin-libdir groHMM.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=groHMM.buildbin-libdir groHMM_1.10.0.tar.gz >groHMM.Rcheck\00install.out 2>&1 && cp groHMM.Rcheck\00install.out groHMM-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=groHMM.buildbin-libdir --install="check:groHMM-install.out" --force-multiarch --no-vignettes --timings groHMM_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/groHMM.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'groHMM/DESCRIPTION' ... OK
* this is package 'groHMM' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'MASS' 'parallel' 'S4Vectors' 'IRanges' 'GenomeInfoDb'
'GenomicRanges' 'GenomicAlignments' 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'groHMM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Minho Chae <minho.chae@gmail.com> [aut, cre]
W. Lee Kraus <lee.kraus@utsouthwestern.edu> [aut, cre]
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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
approx.ratio.CI: no visible global function definition for 'qnorm'
breakTranscriptsOnGenes: no visible global function definition for
'par'
combineTranscripts: no visible global function definition for 'par'
expressedGenes_foreachChrom: no visible global function definition for
'ppois'
getTxDensity: no visible global function definition for 'abline'
pausingIndex_foreachChrom : <anonymous>: no visible global function
definition for 'fisher.test'
plot2Ranges: no visible global function definition for 'plot.new'
plot2Ranges: no visible global function definition for 'plot.window'
plot2Ranges: no visible global function definition for 'rect'
plot2Ranges: no visible global function definition for 'rgb'
plot2Ranges: no visible global function definition for 'text'
plot2Ranges: no visible global function definition for 'title'
plot2Ranges: no visible global function definition for 'axis'
polymeraseWave: no visible global function definition for 'smooth'
polymeraseWave: no visible global function definition for 'hist'
polymeraseWave: no visible global function definition for 'ks.test'
polymeraseWave: no visible global function definition for 'dnorm'
polymeraseWave: no visible global function definition for 'dexp'
polymeraseWave: no visible global function definition for 'dgamma'
readBed: no visible global function definition for 'read.table'
tlsLoess: no visible global function definition for 'loess'
tlsLoess: no visible global function definition for 'predict'
Undefined global functions or variables:
abline axis dexp dgamma dnorm fisher.test hist ks.test loess par
plot.new plot.window ppois predict qnorm read.table rect rgb smooth
text title
Consider adding
importFrom("grDevices", "rgb")
importFrom("graphics", "abline", "axis", "hist", "par", "plot.new",
"plot.window", "rect", "text", "title")
importFrom("stats", "dexp", "dgamma", "dnorm", "fisher.test",
"ks.test", "loess", "ppois", "predict", "qnorm", "smooth")
importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... 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-3.5-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/i386/groHMM.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 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' ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/groHMM.Rcheck/00check.log'
for details.
groHMM.Rcheck/00install.out:
install for i386
* installing *source* package 'groHMM' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c AnnotateProbes.c -o AnnotateProbes.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DecayAlgorithm.c -o DecayAlgorithm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RegisterRRoutines.c -o RegisterRRoutines.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmEM.c -o hmmEM.o
In file included from hmmHeader.h:36:0,
from hmmEM.c:51:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
from hmmFwBw.c:46:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
In file included from hmmHeader.h:36:0,
from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
from hmmViterbi.c:49:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'groHMM' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c AnnotateProbes.c -o AnnotateProbes.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DecayAlgorithm.c -o DecayAlgorithm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RegisterRRoutines.c -o RegisterRRoutines.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmEM.c -o hmmEM.o
In file included from hmmHeader.h:36:0,
from hmmEM.c:51:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
from hmmFwBw.c:46:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
In file included from hmmHeader.h:36:0,
from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
from hmmViterbi.c:49:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'groHMM' as groHMM_1.10.0.zip
* DONE (groHMM)
groHMM.Rcheck/examples_i386/groHMM-Ex.timings:
| name | user | system | elapsed
|
| breakTranscriptsOnGenes | 1.00 | 0.07 | 1.08 |
|
| combineTranscripts | 0.39 | 0.00 | 0.39 |
|
| detectTranscripts | 0.35 | 0.00 | 0.34 |
|
| evaluateHMMInAnnotations | 0.08 | 0.00 | 0.08 |
|
| getCores | 0 | 0 | 0 |
|
| getTxDensity | 0 | 0 | 0 |
|
| limitToXkb | 0.06 | 0.00 | 0.06 |
|
| makeConsensusAnnotations | 0 | 0 | 0 |
|
| metaGene | 0.11 | 0.02 | 0.13 |
|
| pausingIndex | 0.70 | 0.02 | 0.72 |
|
| polymeraseWave | 0.78 | 0.04 | 0.82 |
|
| runMetaGene | 0.02 | 0.00 | 0.02 |
|
| windowAnalysis | 0.47 | 0.02 | 0.48 |
|
| writeWiggle | 0.17 | 0.03 | 0.21 |
|
groHMM.Rcheck/examples_x64/groHMM-Ex.timings:
| name | user | system | elapsed
|
| breakTranscriptsOnGenes | 1.24 | 0.00 | 1.24 |
|
| combineTranscripts | 0.46 | 0.00 | 0.47 |
|
| detectTranscripts | 0.80 | 0.02 | 0.82 |
|
| evaluateHMMInAnnotations | 0.08 | 0.00 | 0.07 |
|
| getCores | 0 | 0 | 0 |
|
| getTxDensity | 0.01 | 0.00 | 0.02 |
|
| limitToXkb | 0.06 | 0.00 | 0.06 |
|
| makeConsensusAnnotations | 0 | 0 | 0 |
|
| metaGene | 0.16 | 0.00 | 0.16 |
|
| pausingIndex | 0.92 | 0.04 | 0.97 |
|
| polymeraseWave | 1.13 | 0.07 | 1.18 |
|
| runMetaGene | 0 | 0 | 0 |
|
| windowAnalysis | 0.18 | 0.03 | 0.22 |
|
| writeWiggle | 0.18 | 0.04 | 0.20 |
|