Michael Love
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/exomeCopy |
| Branch: RELEASE_3_11 |
| Last Commit: 9da198e |
| Last Changed Date: 2020-04-27 14:27:37 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:33 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE exomeCopy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 571/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| exomeCopy 1.34.0 Michael Love
| 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: exomeCopy |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomeCopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings exomeCopy_1.34.0.tar.gz |
| StartedAt: 2020-10-17 03:56:11 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:59:43 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 211.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: exomeCopy.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomeCopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings exomeCopy_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/exomeCopy.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 'exomeCopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'exomeCopy' version '1.34.0'
* 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 'exomeCopy' 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.ExomeCopy
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
emFn : <anonymous>: no visible global function definition for 'dnbinom'
exomeCopy: no visible global function definition for 'lm'
exomeCopy: no visible global function definition for 'optim'
exomeCopy: no visible global function definition for 'new'
exomeCopy: no visible global function definition for 'Rle'
getGCcontent: no visible global function definition for
'letterFrequency'
plot.ExomeCopy: no visible global function definition for 'segments'
plot.ExomeCopy: no visible global function definition for 'legend'
plotCompiledCNV: no visible global function definition for 'axis'
plotCompiledCNV: no visible global function definition for 'segments'
plot,ExomeCopy-missing: no visible global function definition for
'segments'
plot,ExomeCopy-missing: no visible global function definition for
'legend'
Undefined global functions or variables:
Rle axis dnbinom legend letterFrequency lm new optim segments
Consider adding
importFrom("graphics", "axis", "legend", "segments")
importFrom("methods", "new")
importFrom("stats", "dnbinom", "lm", "optim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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-3.11-bioc/R/library/exomeCopy/libs/i386/exomeCopy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/exomeCopy/libs/x64/exomeCopy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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
compileCopyCountSegments 5.28 0.08 5.36
copyCountSegments 5.06 0.01 5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compileCopyCountSegments 5.75 0.02 5.76
copyCountSegments 5.06 0.00 11.56
plotCompiledCNV 4.96 0.02 5.13
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/exomeCopy.Rcheck/00check.log'
for details.
exomeCopy.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/exomeCopy_1.34.0.tar.gz && rm -rf exomeCopy.buildbin-libdir && mkdir exomeCopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomeCopy.buildbin-libdir exomeCopy_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL exomeCopy_1.34.0.zip && rm exomeCopy_1.34.0.tar.gz exomeCopy_1.34.0.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 81412 100 81412 0 0 1197k 0 --:--:-- --:--:-- --:--:-- 1325k
install for i386
* installing *source* package 'exomeCopy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exomeCopy.c -o exomeCopy.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o exomeCopy.dll tmp.def exomeCopy.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/exomeCopy.buildbin-libdir/00LOCK-exomeCopy/00new/exomeCopy/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'exomeCopy'
finding HTML links ... done
ExomeCopy-class html
compileCopyCountSegments html
copyCountSegments html
countBamInGRanges html
finding level-2 HTML links ... done
exomeCopy-package html
exomeCopy html
exomecounts html
generateBackground html
getGCcontent html
negLogLike html
plot.exomeCopyObject html
plotCompiledCNV html
subdivideGRanges 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 'exomeCopy' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exomeCopy.c -o exomeCopy.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o exomeCopy.dll tmp.def exomeCopy.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/exomeCopy.buildbin-libdir/exomeCopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'exomeCopy' as exomeCopy_1.34.0.zip
* DONE (exomeCopy)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'exomeCopy' successfully unpacked and MD5 sums checked
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exomeCopy.Rcheck/examples_i386/exomeCopy-Ex.timings
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exomeCopy.Rcheck/examples_x64/exomeCopy-Ex.timings
|