Laurent Gautier
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/affypdnn |
| Branch: RELEASE_3_9 |
| Last Commit: 83d8b6b |
| Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:19:03 -0400 (Wed, 16 Oct 2019).
| Package 33/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affypdnn 1.58.0 Laurent Gautier
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: affypdnn |
| Version: 1.58.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affypdnn.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings affypdnn_1.58.0.tar.gz |
| StartedAt: 2019-10-16 01:51:46 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:54:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 179.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: affypdnn.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affypdnn.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings affypdnn_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/affypdnn.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affypdnn/DESCRIPTION' ... OK
* this is package 'affypdnn' version '1.58.0'
* 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 'affypdnn' can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.9Mb
sub-directories of 1Mb or more:
data 11.7Mb
* 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 ... NOTE
'library' or 'require' call to 'affy' which was already attached by Depends.
Please remove these calls from your code.
Package in Depends field not imported from: 'affy'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
transform.ProbeSet
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
File 'affypdnn/R/zzz.R':
.onLoad calls:
require(affy)
cat("registering new summary method 'pdnn'.\n")
cat("registering new pmcorrect method 'pdnn' and 'pdnnpredict'.\n")
Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
pmcorrect.pdnn: warning in matrix(as.logical(NA), nr = nrow(probes), nc
= ncol(probes)): partial argument match of 'nr' to 'nrow'
pmcorrect.pdnn: warning in matrix(as.logical(NA), nr = nrow(probes), nc
= ncol(probes)): partial argument match of 'nc' to 'ncol'
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
expressopdnn 27.36 2.64 30.00
generateExprVal.method.pdnn 17.58 2.03 19.62
find.params.pdnn 6.62 0.66 7.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expressopdnn 23.52 2.53 26.06
generateExprVal.method.pdnn 17.86 2.47 20.34
find.params.pdnn 6.81 0.48 7.30
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/affypdnn.Rcheck/00check.log'
for details.
affypdnn.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/affypdnn_1.58.0.tar.gz && rm -rf affypdnn.buildbin-libdir && mkdir affypdnn.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affypdnn.buildbin-libdir affypdnn_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL affypdnn_1.58.0.zip && rm affypdnn_1.58.0.tar.gz affypdnn_1.58.0.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 11.7M 100 11.7M 0 0 35.2M 0 --:--:-- --:--:-- --:--:-- 36.0M
install for i386
* installing *source* package 'affypdnn' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'affypdnn'
finding HTML links ... done
chiptype.pdnn.params html
expressopdnn html
find.params.pdnn html
generateExprVal.method.pdnn html
matplotProbesPDNN html
params.dilution html
pdnn.params.chiptype html
transform.ProbeSet html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
** testing if installed package can be loaded from final location
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'affypdnn' ...
** testing if installed package can be loaded
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
* MD5 sums
packaged installation of 'affypdnn' as affypdnn_1.58.0.zip
* DONE (affypdnn)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'affypdnn' successfully unpacked and MD5 sums checked
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affypdnn.Rcheck/examples_i386/affypdnn-Ex.timings
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affypdnn.Rcheck/examples_x64/affypdnn-Ex.timings
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