Eloi Mercier
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MotIV |
| Branch: RELEASE_3_9 |
| Last Commit: 3ab399d |
| Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:48:00 -0400 (Wed, 16 Oct 2019).
| Package 1045/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MotIV 1.40.0 Eloi Mercier
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: MotIV |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MotIV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MotIV_1.40.0.tar.gz |
| StartedAt: 2019-10-16 04:49:58 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:55:30 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 332.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MotIV.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MotIV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MotIV_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MotIV.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotIV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotIV’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MotIV’ can be installed ... WARNING
Found the following significant warnings:
PlatformSupport.cpp:156:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/MotIV.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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
motifDistances: no visible binding for global variable ‘jaspar.scores’
motifDistances: no visible global function definition for ‘as.dist’
motifMatch: no visible binding for global variable ‘jaspar’
motifMatch: no visible binding for global variable ‘jaspar.scores’
plotDistanceHistogram: no visible global function definition for ‘hist’
plotDistributionHistogram: no visible global function definition for
‘hist’
[,motiv-ANY-ANY-ANY: no visible binding for global variable ‘ANY’
Undefined global functions or variables:
ANY as.dist hist jaspar jaspar.scores
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "as.dist")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'motiv,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MotIV/libs/MotIV.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_rand’, possibly from ‘rand’ (C)
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/MotIV.Rcheck/00check.log’
for details.
MotIV.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MotIV
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MotIV’ ...
** using staged installation
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Alignment.cpp -o Alignment.o
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
int aL_A, aL_B;
^
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
bool for_A, for_B;
^
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
int i1_A, i2_A, i1_B, i2_B;
^
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
Motif* currTwo = two;
^
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
int i1_A, i2_A, i1_B, i2_B;
^
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
double score1, score2, bestScore=0;
^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ColumnComp.cpp -o ColumnComp.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c DeclareAll.cpp -o DeclareAll.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Motif.cpp -o Motif.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp:115:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete(CC);
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp:120:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete(CC);
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp:156:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
currCnt=currCnt;
~~~~~~~^~~~~~~~
PlatformSupport.cpp:112:11: warning: variable 'input' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (inputDB!=0)
^~~~~~~~~~
PlatformSupport.cpp:126:22: note: uninitialized use occurs here
inputName=GET_NAMES(input);
^~~~~
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:149:36: note: expanded from macro 'GET_NAMES'
#define GET_NAMES(x) Rf_getAttrib(x, R_NamesSymbol)
^
PlatformSupport.cpp:112:7: note: remove the 'if' if its condition is always true
else if (inputDB!=0)
^~~~~~~~~~~~~~~
PlatformSupport.cpp:103:23: note: initialize the variable 'input' to silence this warning
SEXP inputName, input;
^
= nullptr
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RandPSSMGen.cpp -o RandPSSMGen.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp:127:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
delete(CC);
^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-MotIV/00new/MotIV/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘MotIV’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MotIV)
MotIV.Rcheck/MotIV-Ex.timings
| name | user | system | elapsed | |
| FOXA_rGADEM | 0.574 | 0.063 | 0.645 | |
| as.data.frame | 0.659 | 0.089 | 0.749 | |
| combineMotifs | 0.661 | 0.063 | 0.724 | |
| exportAsRangedData | 2.800 | 0.210 | 3.012 | |
| exportAsTransfacFile | 0.541 | 0.013 | 0.555 | |
| filter-class | 0.001 | 0.000 | 0.002 | |
| filter-methods | 0.001 | 0.000 | 0.002 | |
| filter | 0.552 | 0.015 | 0.567 | |
| generateDBScores | 0.026 | 0.001 | 0.027 | |
| getGademPWM | 0.273 | 0.021 | 0.293 | |
| jaspar | 0.528 | 0.030 | 0.559 | |
| makePWM | 0.000 | 0.000 | 0.001 | |
| matches-class | 0.001 | 0.000 | 0.001 | |
| motifDistance | 0.529 | 0.023 | 0.555 | |
| motifMatch | 1.549 | 0.077 | 1.652 | |
| motifOccurences | 1.351 | 0.522 | 1.874 | |
| motiv-class | 0.001 | 0.000 | 0.001 | |
| motiv-methods | 0.001 | 0.000 | 0.002 | |
| plot | 3.120 | 0.312 | 3.437 | |
| readGademPWMFile | 0.265 | 0.010 | 0.277 | |
| readPWMfile | 0.026 | 0.001 | 0.028 | |
| seqLogo2 | 0.001 | 0.001 | 0.001 | |
| setFilter | 0.481 | 0.013 | 0.494 | |
| split | 0.514 | 0.010 | 0.527 | |
| tf-class | 0.000 | 0.000 | 0.001 | |
| trimPWMedge | 0.287 | 0.009 | 0.297 | |
| viewAlignment | 0.418 | 0.018 | 0.435 | |
| viewMotifs | 0.469 | 0.018 | 0.487 | |