S. Morganella
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/gaia |
| Branch: RELEASE_3_8 |
| Last Commit: da890c8 |
| Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:27 -0400 (Sat, 13 Apr 2019).
| Package 570/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gaia 2.26.0 S. Morganella
| malbec1 | Linux (Ubuntu 16.04.6 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: gaia |
| Version: 2.26.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaia.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gaia_2.26.0.tar.gz |
| StartedAt: 2019-04-13 02:22:29 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:24:08 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 99.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gaia.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaia.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gaia_2.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/gaia.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gaia/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gaia' version '2.26.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'gaia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
generate_approx_null_hypothesis: no visible global function definition
for 'rbinom'
qvalue: no visible global function definition for 'smooth.spline'
qvalue: no visible global function definition for 'predict'
runGAIA: no visible global function definition for 'write.table'
write_significant_regions: no visible global function definition for
'write.table'
Undefined global functions or variables:
predict rbinom smooth.spline write.table
Consider adding
importFrom("stats", "predict", "rbinom", "smooth.spline")
importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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-3.8-bioc/meat/gaia.Rcheck/00check.log'
for details.
gaia.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/gaia_2.26.0.tar.gz && rm -rf gaia.buildbin-libdir && mkdir gaia.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gaia.buildbin-libdir gaia_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL gaia_2.26.0.zip && rm gaia_2.26.0.tar.gz gaia_2.26.0.zip
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install for i386
* installing *source* package 'gaia' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gaia'
finding HTML links ... done
crc html
crc_markers html
gaia-package html
generate_approx_null_hypothesis html
generate_null_hypothesis html
load_cnv html
load_markers html
peel_off html
qvalue html
runGAIA html
search_peaks_in_regions html
synthCNV_Matrix html
synthMarkers_Matrix html
write_significant_regions html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'gaia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaia' as gaia_2.26.0.zip
* DONE (gaia)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'gaia' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
gaia.Rcheck/examples_i386/gaia-Ex.timings
|
gaia.Rcheck/examples_x64/gaia-Ex.timings
|