Chris Barnes
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/CNVtools |
| Branch: RELEASE_3_10 |
| Last Commit: bf3f720 |
| Last Changed Date: 2019-10-29 13:08:10 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:19:01 -0400 (Wed, 15 Apr 2020).
| Package 330/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNVtools 1.80.0 Chris Barnes
| 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: CNVtools |
| Version: 1.80.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CNVtools_1.80.0.tar.gz |
| StartedAt: 2020-04-15 02:13:19 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:17:24 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 245.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNVtools.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CNVtools_1.80.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CNVtools.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVtools' version '1.80.0'
* 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 'CNVtools' 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 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 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-3.10-bioc/R/library/CNVtools/libs/i386/CNVtools.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-3.10-bioc/R/library/CNVtools/libs/x64/CNVtools.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 or elapsed time > 5s
user system elapsed
CNVtest.select.model 53.54 0.05 53.59
cnv.plot 10.77 0.01 10.78
CNVtest.binary 8.99 0.05 9.08
qt.plot 7.28 0.00 7.28
CNVtest.qt 6.38 0.00 6.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CNVtest.select.model 54.39 0.03 54.58
cnv.plot 10.99 0.00 10.98
CNVtest.binary 10.55 0.01 10.58
qt.plot 7.00 0.00 7.00
CNVtest.qt 6.70 0.02 6.73
* 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-3.10-bioc/meat/CNVtools.Rcheck/00check.log'
for details.
CNVtools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CNVtools_1.80.0.tar.gz && rm -rf CNVtools.buildbin-libdir && mkdir CNVtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVtools.buildbin-libdir CNVtools_1.80.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CNVtools_1.80.0.zip && rm CNVtools_1.80.0.tar.gz CNVtools_1.80.0.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 466k 100 466k 0 0 9428k 0 --:--:-- --:--:-- --:--:-- 9.9M
install for i386
* installing *source* package 'CNVtools' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c fitmodel.cpp -o fitmodel.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c glm_test.cpp -o glm_test.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c mla.cpp -o mla.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c routine.cpp -o routine.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c zeroin.c -o zeroin.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CNVtools.dll tmp.def fitmodel.o glm_test.o mla.o routine.o zeroin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CNVtools.buildbin-libdir/00LOCK-CNVtools/00new/CNVtools/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNVtools'
finding HTML links ... done
A112 html
CNV.fitModel html
CNVtest.binary html
CNVtest.binary.T html
CNVtest.qt html
CNVtest.qt.T html
CNVtest.select.model html
CNVtools-package html
EM.starting.point html
ExpandData html
apply.ldf html
apply.pca html
cnv.plot html
compact.data.frame html
get.model.spec html
getQualityScore html
getparams html
qt.plot html
test.posterior 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 'CNVtools' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c fitmodel.cpp -o fitmodel.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c glm_test.cpp -o glm_test.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c mla.cpp -o mla.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c routine.cpp -o routine.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c zeroin.c -o zeroin.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CNVtools.dll tmp.def fitmodel.o glm_test.o mla.o routine.o zeroin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CNVtools.buildbin-libdir/CNVtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVtools' as CNVtools_1.80.0.zip
* DONE (CNVtools)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CNVtools' successfully unpacked and MD5 sums checked
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CNVtools.Rcheck/examples_i386/CNVtools-Ex.timings
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CNVtools.Rcheck/examples_x64/CNVtools-Ex.timings
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