Zhi Yang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/HiLDA |
| Branch: RELEASE_3_11 |
| Last Commit: a23fd31 |
| Last Changed Date: 2020-04-27 15:28:42 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:49 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE HiLDA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 822/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HiLDA 1.2.0 Zhi Yang
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: HiLDA |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiLDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HiLDA_1.2.0.tar.gz |
| StartedAt: 2020-10-17 04:55:38 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:05:59 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 621.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiLDA.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiLDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HiLDA_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiLDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiLDA' version '1.2.0'
* package encoding: UTF-8
* 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 'HiLDA' 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
* 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 ... 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 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-3.11-bioc/R/library/HiLDA/libs/i386/HiLDA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/HiLDA/libs/x64/HiLDA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
hildaTest 54.05 0.08 152.58
hildaGlobalResult 34.07 0.08 89.53
hildaReadMPFile 13.65 1.56 81.15
hildaBarplot 1.18 0.01 7.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
hildaTest 52.03 0.04 52.08
hildaGlobalResult 35.41 0.04 47.50
hildaReadMPFile 14.14 0.64 18.21
hildaDiffPlot 0.85 0.00 22.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck/00check.log'
for details.
HiLDA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/HiLDA_1.2.0.tar.gz && rm -rf HiLDA.buildbin-libdir && mkdir HiLDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiLDA.buildbin-libdir HiLDA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL HiLDA_1.2.0.zip && rm HiLDA_1.2.0.tar.gz HiLDA_1.2.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2120k 100 2120k 0 0 25.3M 0 --:--:-- --:--:-- --:--:-- 27.6M
install for i386
* installing *source* package 'HiLDA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EMalgorithm.cpp -o EMalgorithm.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkBoundary.cpp -o checkBoundary.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convertFromToVector.cpp -o convertFromToVector.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o HiLDA.dll tmp.def EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.buildbin-libdir/00LOCK-HiLDA/00new/HiLDA/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HiLDA'
finding HTML links ... done
EstimatedParameters-class html
MetaInformation-class html
MutationFeatureData-class html
PMSboundary html
boundaryTurbo_F html
boundaryTurbo_Q html
calcPMSLikelihood html
convertFromTurbo_F html
convertFromTurbo_Q html
convertToTurbo_F html
convertToTurbo_Q html
getLogLikelihoodC html
getMutationFeatureVector html
hildaBarplot html
hildaDiffPlot html
hildaGlobalResult html
hildaLocalResult html
hildaPlotSignature html
hildaReadMPFile html
hildaRhat html
hildaTest html
mySquareEM html
pmBarplot html
pmMultiBarplot html
pmPlotSignature html
pmgetSignature html
updateMstepFQC html
updatePMSParam html
updateTheta_NormalizedC html
visPMS html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'HiLDA' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EMalgorithm.cpp -o EMalgorithm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkBoundary.cpp -o checkBoundary.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convertFromToVector.cpp -o convertFromToVector.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o HiLDA.dll tmp.def EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.buildbin-libdir/HiLDA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiLDA' as HiLDA_1.2.0.zip
* DONE (HiLDA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'HiLDA' successfully unpacked and MD5 sums checked
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HiLDA.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(HiLDA)
Loading required package: ggplot2
>
> test_check("HiLDA")
#trial: 1; #iteration: 19; time(s): 0.06; convergence: TRUE; loglikelihood: -8202.3185
#trial: 2; #iteration: 16; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3184
#trial: 3; #iteration: 26; time(s): 0.06; convergence: TRUE; loglikelihood: -8202.3184
#trial: 4; #iteration: 15; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3334
#trial: 5; #iteration: 49; time(s): 0.11; convergence: TRUE; loglikelihood: -8202.3200
#trial: 6; #iteration: 15; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3333
#trial: 7; #iteration: 18; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3185
#trial: 8; #iteration: 19; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3330
#trial: 9; #iteration: 25; time(s): 0.06; convergence: TRUE; loglikelihood: -8202.3199
#trial: 10; #iteration: 35; time(s): 0.07; convergence: TRUE; loglikelihood: -8202.3200
== testthat results ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
3.50 0.23 3.71
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HiLDA.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(HiLDA)
Loading required package: ggplot2
>
> test_check("HiLDA")
#trial: 1; #iteration: 39; time(s): 0.11; convergence: TRUE; loglikelihood: -8202.3184
#trial: 2; #iteration: 11; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3183
#trial: 3; #iteration: 15; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3185
#trial: 4; #iteration: 15; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3186
#trial: 5; #iteration: 62; time(s): 0.13; convergence: TRUE; loglikelihood: -8202.3185
#trial: 6; #iteration: 25; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3185
#trial: 7; #iteration: 12; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3186
#trial: 8; #iteration: 55; time(s): 0.09; convergence: TRUE; loglikelihood: -8202.3200
#trial: 9; #iteration: 21; time(s): 0.06; convergence: TRUE; loglikelihood: -8202.3184
#trial: 10; #iteration: 14; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3185
== testthat results ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
2.98 0.21 3.39
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HiLDA.Rcheck/examples_i386/HiLDA-Ex.timings
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HiLDA.Rcheck/examples_x64/HiLDA-Ex.timings
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