Aaron Taudt
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/methimpute |
| Branch: RELEASE_3_10 |
| Last Commit: 67c8034 |
| Last Changed Date: 2019-10-29 13:10:49 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:46:11 -0400 (Wed, 15 Apr 2020).
| Package 1013/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methimpute 1.8.0 Aaron Taudt
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: methimpute |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methimpute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methimpute_1.8.0.tar.gz |
| StartedAt: 2020-04-15 03:43:57 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:47:06 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 189.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methimpute.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methimpute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methimpute_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/methimpute.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methimpute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methimpute’ version ‘1.8.0’
* 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 ‘methimpute’ 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
* 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 ... 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 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotting 23.492 0.499 22.892
extractCytosinesFromFASTA 8.751 0.213 9.043
callMethylationSeparate 5.881 0.425 5.016
collapseBins 4.901 0.056 5.001
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/methimpute.Rcheck/00check.log’
for details.
methimpute.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methimpute
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘methimpute’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c densities.cpp -o densities.o
In file included from densities.cpp:1:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(int test, int total);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
virtual double getLogDensityAt(int) { return(0); };
^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(double x);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
virtual double getLogDensityAt(int) { return(0); };
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c fitHMM.cpp -o fitHMM.o
In file included from fitHMM.cpp:2:
In file included from ./scalehmm.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(int test, int total);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
virtual double getLogDensityAt(int) { return(0); };
^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(double x);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
virtual double getLogDensityAt(int) { return(0); };
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c fitHMM_context.cpp -o fitHMM_context.o
In file included from fitHMM_context.cpp:2:
In file included from ./hmm_context.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(int test, int total);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
virtual double getLogDensityAt(int) { return(0); };
^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(double x);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
virtual double getLogDensityAt(int) { return(0); };
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c hmm_context.cpp -o hmm_context.o
In file included from hmm_context.cpp:1:
In file included from ./hmm_context.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(int test, int total);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
virtual double getLogDensityAt(int) { return(0); };
^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(double x);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
virtual double getLogDensityAt(int) { return(0); };
^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c methimpute_init.c -o methimpute_init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o
In file included from scalehmm.cpp:1:
In file included from ./scalehmm.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(int test, int total);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
virtual double getLogDensityAt(int) { return(0); };
^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
double getLogDensityAt(double x);
^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
virtual double getLogDensityAt(int) { return(0); };
^
2 warnings 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 methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-methimpute/00new/methimpute/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (methimpute)
methimpute.Rcheck/methimpute-Ex.timings
| name | user | system | elapsed | |
| arabidopsis_TEs | 0.097 | 0.002 | 0.101 | |
| arabidopsis_chromosomes | 0.005 | 0.003 | 0.008 | |
| arabidopsis_genes | 0.024 | 0.002 | 0.026 | |
| arabidopsis_toydata | 0.234 | 0.016 | 0.252 | |
| binning | 3.630 | 0.305 | 3.961 | |
| binomialTestMethylation | 0.272 | 0.032 | 0.307 | |
| callMethylation | 3.963 | 0.201 | 2.774 | |
| callMethylationSeparate | 5.881 | 0.425 | 5.016 | |
| collapseBins | 4.901 | 0.056 | 5.001 | |
| distanceCorrelation | 1.994 | 0.106 | 2.121 | |
| estimateTransDist | 2.059 | 0.095 | 2.169 | |
| exportMethylome | 0.000 | 0.000 | 0.001 | |
| extractCytosinesFromFASTA | 8.751 | 0.213 | 9.043 | |
| getDistinctColors | 0.055 | 0.005 | 0.060 | |
| getStateColors | 0.026 | 0.000 | 0.026 | |
| import | 0.947 | 0.070 | 0.864 | |
| importRene | 0.075 | 0.002 | 0.077 | |
| inflateMethylome | 0.741 | 0.077 | 0.643 | |
| loadFromFiles | 0.534 | 0.023 | 0.561 | |
| plotting | 23.492 | 0.499 | 22.892 | |