| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the OncoSimulR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OncoSimulR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1308/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 3.0.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: OncoSimulR |
| Version: 3.0.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OncoSimulR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz |
| StartedAt: 2021-10-15 02:55:41 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:12:09 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 987.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OncoSimulR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OncoSimulR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OncoSimulR' version '3.0.0'
* 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 whether package 'OncoSimulR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 17.4Mb
sub-directories of 1Mb or more:
exec 2.2Mb
libs 14.1Mb
* 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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... 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-3.13-bioc/R/library/OncoSimulR/libs/i386/OncoSimulR.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-3.13-bioc/R/library/OncoSimulR/libs/x64/OncoSimulR.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
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/OncoSimulR_3.0.0.tar.gz && rm -rf OncoSimulR.buildbin-libdir && mkdir OncoSimulR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OncoSimulR.buildbin-libdir OncoSimulR_3.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL OncoSimulR_3.0.0.zip && rm OncoSimulR_3.0.0.tar.gz OncoSimulR_3.0.0.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
94 1262k 94 1189k 0 0 2214k 0 --:--:-- --:--:-- --:--:-- 2214k
100 1262k 100 1262k 0 0 2335k 0 --:--:-- --:--:-- --:--:-- 2333k
install for i386
* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/random.c -o FitnessLandscape/random.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/input.c -o FitnessLandscape/input.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
FitnessLandscape/LinearAlgebra.c: In function 'svdcmp':
FitnessLandscape/LinearAlgebra.c:640:27: warning: 'l' may be used uninitialized in this function [-Wmaybe-uninitialized]
v[j][i]=(u[i][j]/u[i][l])/g;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/models.c -o FitnessLandscape/models.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
"C:/rtools40/mingw32/bin/"ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
C:\rtools40\mingw32\bin\ar.exe: creating liblandscape.a
"C:/rtools40/mingw32/bin/"ranlib liblandscape.a;
"C:/rtools40/mingw32/bin/"gcc -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
"C:/rtools40/mingw32/bin/"gcc -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c BNB_nr.cpp -o BNB_nr.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c OncoSimulR_init.c -o OncoSimulR_init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c accessible_genotypes.cpp -o accessible_genotypes.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c bnb_common.cpp -o bnb_common.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c new_restrict.cpp -o new_restrict.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o OncoSimulR.dll tmp.def BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -Wa,-mbig-obj -O3 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing via 'install.libs.R' to C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/i386"
Installing fl_statistics.exe fl_generate.exe to C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/exec/i386
Installing library OncoSimulR.dll to C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'OncoSimulR'
finding HTML links ... done
OncoSimulWide2Long html
POM html
allFitnessEffects html
benchmarks html
evalAllGenotypes html
example-missing-drivers html
examplePosets html
examplesFitnessEffects html
freq-dep-simul-examples html
mcfLs html
oncoSimulIndiv html
plot.fitnessEffects html
plot.oncosimul html
finding level-2 HTML links ... done
plotClonePhylog html
plotFitnessLandscape html
plotPoset html
poset html
rfitness html
samplePop html
simOGraph html
to_Magellan 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 'OncoSimulR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/random.c -o FitnessLandscape/random.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/input.c -o FitnessLandscape/input.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
FitnessLandscape/LinearAlgebra.c: In function 'svdcmp':
FitnessLandscape/LinearAlgebra.c:640:27: warning: 'l' may be used uninitialized in this function [-Wmaybe-uninitialized]
v[j][i]=(u[i][j]/u[i][l])/g;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/models.c -o FitnessLandscape/models.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
"C:/rtools40/mingw64/bin/"ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
C:\rtools40\mingw64\bin\ar.exe: creating liblandscape.a
"C:/rtools40/mingw64/bin/"ranlib liblandscape.a;
"C:/rtools40/mingw64/bin/"gcc -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
"C:/rtools40/mingw64/bin/"gcc -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c BNB_nr.cpp -o BNB_nr.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c OncoSimulR_init.c -o OncoSimulR_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c accessible_genotypes.cpp -o accessible_genotypes.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c bnb_common.cpp -o bnb_common.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -O3 -c new_restrict.cpp -o new_restrict.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o OncoSimulR.dll tmp.def BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -Wa,-mbig-obj -O3 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing via 'install.libs.R' to C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to C:/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.buildbin-libdir/OncoSimulR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OncoSimulR' as OncoSimulR_3.0.0.zip
* DONE (OncoSimulR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'OncoSimulR' successfully unpacked and MD5 sums checked
|
OncoSimulR.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(OncoSimulR)
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Fri Oct 15 02:59:36 2021
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Fri Oct 15 02:59:38 2021
Took 1.77
Starting LOD_POM at Fri Oct 15 02:59:38 2021
Ending LOD_POM at Fri Oct 15 02:59:57 2021
Took 19.02
Starting test.Z-all-fitness at Fri Oct 15 02:59:57 2021
Ending test.Z-all-fitness at Fri Oct 15 02:59:57 2021
Took 0.06
Starting test.Z-driver-counts at Fri Oct 15 02:59:57 2021
Ending test.Z-driver-counts at Fri Oct 15 02:59:57 2021
Took 0.16
Starting test.Z-fixation at Fri Oct 15 02:59:57 2021
Ending test.Z-fixation at Fri Oct 15 02:59:58 2021
Took 0.89
Starting test.Z-magellan at Fri Oct 15 02:59:58 2021
Ended test.Z-magellan at Fri Oct 15 03:00:00 2021
Starting test.Z-mutator at Fri Oct 15 03:00:00 2021
Ending test.Z-mutator at Fri Oct 15 03:00:01 2021
Took 0.42
Starting test.Z-mutatorFDF at Fri Oct 15 03:00:01 2021
Ending test.Z-mutatorFDF at Fri Oct 15 03:00:01 2021
Took 0.11
Starting test.Z-oncoSimulIndiv at Fri Oct 15 03:00:01 2021
Ending test.Z-oncoSimulIndiv at Fri Oct 15 03:00:02 2021
Took 1.44
Starting test.Z-oncoSimulIndivFDF at Fri Oct 15 03:00:02 2021
Ending test.Z-oncoSimulIndivFDF at Fri Oct 15 03:00:02 2021
Took 0.12
Starting test.Z-rfitness-landscape at Fri Oct 15 03:00:02 2021
Ending test.Z-rfitness-landscape at Fri Oct 15 03:00:03 2021
Took 0.11
Starting Z-sample-only-last tests Fri Oct 15 03:00:03 2021
Ending Z-sample-only-last tests Fri Oct 15 03:00:03 2021
Took 0
Starting Z-total-present-drivers tests Fri Oct 15 03:00:03 2021
Ending Z-total-present-drivers tests Fri Oct 15 03:00:04 2021
Took 1.23
Dummy empty test Fri Oct 15 03:00:04 2021
Starting accessible_genotypes at Fri Oct 15 03:00:04 2021
Ending accessible_genotypes at Fri Oct 15 03:00:09 2021
Took 5.34
Starting all fitness at Fri Oct 15 03:00:09 2021
Ending all-fitness at Fri Oct 15 03:00:13 2021
Took 4.25
Starting test.allFitnessEffectsFDF at Fri Oct 15 03:00:13 2021
Ending test.allFitnessEffectsFDF at Fri Oct 15 03:00:14 2021
Took 0.11
Starting test.allFitnessEffectsFDF at Fri Oct 15 03:00:14 2021
Ending test.allFitnessEffectsFDF at Fri Oct 15 03:00:14 2021
Took 0.3
Starting driverCounts at Fri Oct 15 03:00:14 2021
Ending driverCounts at Fri Oct 15 03:00:20 2021
Took 6.47
Starting epist-order-modules at Fri Oct 15 03:00:20 2021
Ending epist-order-modules at Fri Oct 15 03:00:20 2021
Took 0.03
Starting test.evaluatingGenotypesFDF at Fri Oct 15 03:00:20 2021
Ending test.evaluatingGenotypesFDF at Fri Oct 15 03:00:21 2021
Took 0.16
Starting exercise-plotting-code at Fri Oct 15 03:00:21 2021
Ending exercise-plotting-code at Fri Oct 15 03:00:29 2021
Took 8.25
Starting exercise-rfitness at Fri Oct 15 03:00:29 2021
Ending exercise-rfitness at Fri Oct 15 03:00:39 2021
Took 10.2
Starting to_Magella at Fri Oct 15 03:00:39 2021
Ending to_Magella at Fri Oct 15 03:00:39 2021
Took 0.05
Starting fitness preds at Fri Oct 15 03:00:39 2021
Observed vs expected, case III
done tries 1
Ending fitness preds long at Fri Oct 15 03:00:54 2021
Took 15.16
Starting fixation at Fri Oct 15 03:00:54 2021
Ending fixation at Fri Oct 15 03:01:47 2021
Took 53.08
Starting test.flfast-additional.R test at Fri Oct 15 03:01:47 2021
Ending test.flfast-additional.R test at Fri Oct 15 03:01:49 2021
Took 1.75
Starting test.flfast-mutator.R test at Fri Oct 15 03:01:49 2021
Finished test.flfast-mutator.R test at Fri Oct 15 03:01:53 2021
Took 3.52
Starting genotFitness at Fri Oct 15 03:01:53 2021
Ending genotFitness at Fri Oct 15 03:01:53 2021
Took 0.14
Starting genot_fitness_to_epistasis at Fri Oct 15 03:01:53 2021
Ending genot_fitness_to_epistasis at Fri Oct 15 03:01:53 2021
Took 0.02
Starting init-mutant tests Fri Oct 15 03:01:53 2021
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Fri Oct 15 03:02:04 2021
Took 11.11
Starting test.magellan at Fri Oct 15 03:02:04 2021
Ending test.magellan at Fri Oct 15 03:02:05 2021
Took 0.73
Starting test.modules-root-no-root at Fri Oct 15 03:02:05 2021
Ending test.modules-root-no-root at Fri Oct 15 03:02:05 2021
Took 0.09
Starting at mutPropGrowth Fri Oct 15 03:02:05 2021
Ended test.mutPropGrowth: Fri Oct 15 03:02:17 2021
Took 12.2
Starting test.mutator-oncoSimulSample.R test at Fri Oct 15 03:02:17 2021
Finished test.mutator-oncoSimulSample.R test at Fri Oct 15 03:02:27 2021
Took 10.08 seconds
Starting test.mutator.R test at Fri Oct 15 03:02:27 2021[1] 1.778058e-08
[1] 8.985416e-13
Finished test.mutator.R test at Fri Oct 15 03:02:50 2021
Took 23.31
Starting test.mutatorFDF.R test at Fri Oct 15 03:02:50 2021
Starting test.no-v1 at Fri Oct 15 03:02:51 2021
Ending test.no-v1 at Fri Oct 15 03:02:51 2021
Took 0.02
Starting oncoSimulIndiv-miscell tests Fri Oct 15 03:02:51 2021
Ending oncoSimulIndiv-miscell tests Fri Oct 15 03:02:59 2021
Took 8.2
Starting oncoSimulSample-failures tests Fri Oct 15 03:02:59 2021
Ending oncoSimulSample-failures tests Fri Oct 15 03:03:03 2021
Took 3.52
Starting oncoSimulSample-limits tests Fri Oct 15 03:03:03 2021
Ending oncoSimulSample-limits tests Fri Oct 15 03:03:03 2021
Took 0.05
Starting per-gene-mutation rates at Fri Oct 15 03:03:03 2021
Ending per-gene-mutation rates at Fri Oct 15 03:03:51 2021
Took 48.33
Starting plotFitnessLandscape at Fri Oct 15 03:03:51 2021
Ending plotFitnessLandscape at Fri Oct 15 03:03:54 2021
Took 3.11
Starting poset-transformations tests Fri Oct 15 03:03:54 2021
Ending poset-transformations tests Fri Oct 15 03:04:00 2021
Took 6.13
Starting sample-prob Fri Oct 15 03:04:00 2021
[1] 9.136237e-11
[1] 2.828492e-11
[1] 3.031847e-09
[1] 1.965889e-12
[1] 3.249734e-14
[1] 6.772691e-11
[1] 5.098341e-08
[1] 1.386592e-12
[1] 1.281147e-06
[1] 2.288254e-13
[1] 2.086568e-09
[1] 1.205347e-10
Ending sample-prob tests Fri Oct 15 03:04:10 2021
Took 9.47
Starting samplePop tests Fri Oct 15 03:04:10 2021
Ending samplePop tests Fri Oct 15 03:04:23 2021
Took 13.28
Starting simuls-runs-examples tests Fri Oct 15 03:04:23 2021
Ending simuls-runs-examples tests Fri Oct 15 03:04:43 2021
Took 20.09
Starting warning-mutPropGrowth tests Fri Oct 15 03:04:43 2021
Ending warning-mutPropGrowth tests Fri Oct 15 03:04:44 2021
Took 1.33
Starting wide2long tests Fri Oct 15 03:04:44 2021
Ending wide2long tests Fri Oct 15 03:04:45 2021
Took 0.45
== Skipped tests ===============================================================
* On Windows (1)
* empty test (5)
[ FAIL 0 | WARN 1 | SKIP 6 | PASS 8203 ]
>
> proc.time()
user system elapsed
304.87 1.43 313.42
|
OncoSimulR.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(OncoSimulR)
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Fri Oct 15 03:04:50 2021
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Fri Oct 15 03:04:51 2021
Took 0.63
Starting LOD_POM at Fri Oct 15 03:04:51 2021
Ending LOD_POM at Fri Oct 15 03:05:10 2021
Took 19.38
Starting test.Z-all-fitness at Fri Oct 15 03:05:10 2021
Ending test.Z-all-fitness at Fri Oct 15 03:05:10 2021
Took 0.08
Starting test.Z-driver-counts at Fri Oct 15 03:05:10 2021
Ending test.Z-driver-counts at Fri Oct 15 03:05:10 2021
Took 0.17
Starting test.Z-fixation at Fri Oct 15 03:05:10 2021
Ending test.Z-fixation at Fri Oct 15 03:05:11 2021
Took 0.64
Starting test.Z-magellan at Fri Oct 15 03:05:11 2021
Ended test.Z-magellan at Fri Oct 15 03:05:13 2021
Starting test.Z-mutator at Fri Oct 15 03:05:13 2021
Ending test.Z-mutator at Fri Oct 15 03:05:14 2021
Took 0.41
Starting test.Z-mutatorFDF at Fri Oct 15 03:05:14 2021
Ending test.Z-mutatorFDF at Fri Oct 15 03:05:14 2021
Took 0.11
Starting test.Z-oncoSimulIndiv at Fri Oct 15 03:05:14 2021
Ending test.Z-oncoSimulIndiv at Fri Oct 15 03:05:15 2021
Took 1.47
Starting test.Z-oncoSimulIndivFDF at Fri Oct 15 03:05:15 2021
Ending test.Z-oncoSimulIndivFDF at Fri Oct 15 03:05:15 2021
Took 0.16
Starting test.Z-rfitness-landscape at Fri Oct 15 03:05:15 2021
Ending test.Z-rfitness-landscape at Fri Oct 15 03:05:16 2021
Took 0.14
Starting Z-sample-only-last tests Fri Oct 15 03:05:16 2021
Ending Z-sample-only-last tests Fri Oct 15 03:05:16 2021
Took 0
Starting Z-total-present-drivers tests Fri Oct 15 03:05:16 2021
Ending Z-total-present-drivers tests Fri Oct 15 03:05:17 2021
Took 1.44
Dummy empty test Fri Oct 15 03:05:17 2021
Starting accessible_genotypes at Fri Oct 15 03:05:17 2021
Ending accessible_genotypes at Fri Oct 15 03:05:23 2021
Took 5.59
Starting all fitness at Fri Oct 15 03:05:23 2021
Ending all-fitness at Fri Oct 15 03:05:27 2021
Took 4.2
Starting test.allFitnessEffectsFDF at Fri Oct 15 03:05:27 2021
Ending test.allFitnessEffectsFDF at Fri Oct 15 03:05:27 2021
Took 0.13
Starting test.allFitnessEffectsFDF at Fri Oct 15 03:05:27 2021
Ending test.allFitnessEffectsFDF at Fri Oct 15 03:05:27 2021
Took 0.34
Starting driverCounts at Fri Oct 15 03:05:27 2021
Ending driverCounts at Fri Oct 15 03:05:34 2021
Took 7.17
Starting epist-order-modules at Fri Oct 15 03:05:34 2021
Ending epist-order-modules at Fri Oct 15 03:05:35 2021
Took 0.02
Starting test.evaluatingGenotypesFDF at Fri Oct 15 03:05:35 2021
Ending test.evaluatingGenotypesFDF at Fri Oct 15 03:05:35 2021
Took 0.2
Starting exercise-plotting-code at Fri Oct 15 03:05:35 2021
Ending exercise-plotting-code at Fri Oct 15 03:05:44 2021
Took 9.72
Starting exercise-rfitness at Fri Oct 15 03:05:44 2021
Ending exercise-rfitness at Fri Oct 15 03:05:54 2021
Took 9.56
Starting to_Magella at Fri Oct 15 03:05:54 2021
Ending to_Magella at Fri Oct 15 03:05:54 2021
Took 0.02
Starting fitness preds at Fri Oct 15 03:05:54 2021
Observed vs expected, case III
done tries 1
Ending fitness preds long at Fri Oct 15 03:06:07 2021
Took 12.44
Starting fixation at Fri Oct 15 03:06:07 2021
Ending fixation at Fri Oct 15 03:07:09 2021
Took 62.05
Starting test.flfast-additional.R test at Fri Oct 15 03:07:09 2021
Ending test.flfast-additional.R test at Fri Oct 15 03:07:48 2021
Took 39.87
Starting test.flfast-mutator.R test at Fri Oct 15 03:07:48 2021
Finished test.flfast-mutator.R test at Fri Oct 15 03:07:51 2021
Took 2.05
Starting genotFitness at Fri Oct 15 03:07:51 2021
Ending genotFitness at Fri Oct 15 03:07:51 2021
Took 0.14
Starting genot_fitness_to_epistasis at Fri Oct 15 03:07:51 2021
Ending genot_fitness_to_epistasis at Fri Oct 15 03:07:51 2021
Took 0.03
Starting init-mutant tests Fri Oct 15 03:07:51 2021
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Fri Oct 15 03:08:06 2021
Took 15.61
Starting test.magellan at Fri Oct 15 03:08:06 2021
Ending test.magellan at Fri Oct 15 03:08:07 2021
Took 0.63
Starting test.modules-root-no-root at Fri Oct 15 03:08:07 2021
Ending test.modules-root-no-root at Fri Oct 15 03:08:07 2021
Took 0.09
Starting at mutPropGrowth Fri Oct 15 03:08:07 2021
Ended test.mutPropGrowth: Fri Oct 15 03:08:29 2021
Took 21.65
Starting test.mutator-oncoSimulSample.R test at Fri Oct 15 03:08:29 2021
Finished test.mutator-oncoSimulSample.R test at Fri Oct 15 03:08:46 2021
Took 17.75 seconds
Starting test.mutator.R test at Fri Oct 15 03:08:47 2021[1] 1.11994e-07
[1] 3.264506e-11
Finished test.mutator.R test at Fri Oct 15 03:09:19 2021
Took 32.06
Starting test.mutatorFDF.R test at Fri Oct 15 03:09:19 2021
Starting test.no-v1 at Fri Oct 15 03:09:19 2021
Ending test.no-v1 at Fri Oct 15 03:09:19 2021
Took 0.02
Starting oncoSimulIndiv-miscell tests Fri Oct 15 03:09:19 2021
Ending oncoSimulIndiv-miscell tests Fri Oct 15 03:09:28 2021
Took 8.45
Starting oncoSimulSample-failures tests Fri Oct 15 03:09:28 2021
Ending oncoSimulSample-failures tests Fri Oct 15 03:09:32 2021
Took 3.81
Starting oncoSimulSample-limits tests Fri Oct 15 03:09:32 2021
Ending oncoSimulSample-limits tests Fri Oct 15 03:09:32 2021
Took 0.06
Starting per-gene-mutation rates at Fri Oct 15 03:09:32 2021
Ending per-gene-mutation rates at Fri Oct 15 03:10:34 2021
Took 62.53
Starting plotFitnessLandscape at Fri Oct 15 03:10:34 2021
Ending plotFitnessLandscape at Fri Oct 15 03:10:38 2021
Took 4.3
Starting poset-transformations tests Fri Oct 15 03:10:38 2021
Ending poset-transformations tests Fri Oct 15 03:10:48 2021
Took 9.73
Starting sample-prob Fri Oct 15 03:10:48 2021
[1] 6.223479e-13
[1] 7.318951e-07
[1] 1.472683e-11
[1] 3.136845e-12
[1] 9.954945e-06
[1] 1.099808e-14
[1] 1.622587e-08
[1] 7.907193e-11
[1] 2.179951e-09
[1] 1.295198e-13
[1] 1.988511e-10
[1] 1.334744e-10
Ending sample-prob tests Fri Oct 15 03:11:09 2021
Took 20.45
Starting samplePop tests Fri Oct 15 03:11:09 2021
Ending samplePop tests Fri Oct 15 03:11:32 2021
Took 23.61
Starting simuls-runs-examples tests Fri Oct 15 03:11:32 2021
Ending simuls-runs-examples tests Fri Oct 15 03:11:50 2021
Took 17.56
Starting warning-mutPropGrowth tests Fri Oct 15 03:11:50 2021
Ending warning-mutPropGrowth tests Fri Oct 15 03:11:53 2021
Took 2.83
Starting wide2long tests Fri Oct 15 03:11:53 2021
Ending wide2long tests Fri Oct 15 03:11:53 2021
Took 0.45
== Skipped tests ===============================================================
* On Windows (1)
* empty test (5)
[ FAIL 0 | WARN 1 | SKIP 6 | PASS 8176 ]
>
> proc.time()
user system elapsed
362.07 1.64 428.15
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OncoSimulR.Rcheck/examples_i386/OncoSimulR-Ex.timings
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OncoSimulR.Rcheck/examples_x64/OncoSimulR-Ex.timings
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