BioC 3.3: CHECK report for MinimumDistance on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:01 -0400 (Tue, 27 Oct 2015).
MinimumDistance 1.15.0
Robert B Scharpf
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: MinimumDistance
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| Version: 1.15.0
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| Command: rm -rf MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && mkdir MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.15.0.tar.gz >MinimumDistance.Rcheck\00install.out 2>&1 && cp MinimumDistance.Rcheck\00install.out MinimumDistance-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.15.0.tar.gz
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| StartedAt: 2015-10-27 04:11:15 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 04:17:29 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 374.5 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: MinimumDistance.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && mkdir MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.15.0.tar.gz >MinimumDistance.Rcheck\00install.out 2>&1 && cp MinimumDistance.Rcheck\00install.out MinimumDistance-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.15.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/MinimumDistance.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MinimumDistance' version '1.15.0'
* 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 'MinimumDistance' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
calculateMindist,list: no visible binding for global variable 'elt'
Undefined global functions or variables:
elt
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [16s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pedigreeGrid 5.22 0.05 5.26
** running examples for arch 'x64' ... [18s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pedigreeGrid 5.19 0 5.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRUnit.R' [57s]
[57s] OK
** running tests for arch 'x64' ...
Running 'doRUnit.R' [59s]
[59s] 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:/biocbld/bbs-3.3-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.
MinimumDistance.Rcheck/00install.out:
install for i386
* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'allNames' in package 'MinimumDistance'
Creating a generic function for 'colMads' from package 'matrixStats' in package 'MinimumDistance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.15.0.zip
* DONE (MinimumDistance)
MinimumDistance.Rcheck/examples_i386/MinimumDistance-Ex.timings:
| name | user | system | elapsed
|
| DNAcopyParam | 0.02 | 0.00 | 0.01 |
|
| FilterParamMD | 2.30 | 0.06 | 2.36 |
|
| MAP2 | 0.04 | 0.00 | 0.05 |
|
| MDRanges-class | 0.03 | 0.00 | 0.03 |
|
| MinDistGRanges-class | 0.1 | 0.0 | 0.1 |
|
| MinDistGRanges | 0.01 | 0.00 | 0.01 |
|
| ParentOffspring-class | 0.02 | 0.00 | 0.02 |
|
| ParentOffspringList-class | 0 | 0 | 0 |
|
| Pedigree | 0 | 0 | 0 |
|
| TrioSet | 1.81 | 0.01 | 1.92 |
|
| acf2 | 0 | 0 | 0 |
|
| md_exp | 0 | 0 | 0 |
|
| pedigreeGrid | 5.22 | 0.05 | 5.26 |
|
| pedigreeViewports | 0 | 0 | 0 |
|
MinimumDistance.Rcheck/examples_x64/MinimumDistance-Ex.timings:
| name | user | system | elapsed
|
| DNAcopyParam | 0.02 | 0.00 | 0.01 |
|
| FilterParamMD | 2.26 | 0.03 | 2.30 |
|
| MAP2 | 0.05 | 0.00 | 0.04 |
|
| MDRanges-class | 0.01 | 0.00 | 0.02 |
|
| MinDistGRanges-class | 0.09 | 0.01 | 0.11 |
|
| MinDistGRanges | 0.03 | 0.00 | 0.03 |
|
| ParentOffspring-class | 0 | 0 | 0 |
|
| ParentOffspringList-class | 0 | 0 | 0 |
|
| Pedigree | 0.00 | 0.02 | 0.01 |
|
| TrioSet | 2.52 | 0.03 | 2.55 |
|
| acf2 | 0 | 0 | 0 |
|
| md_exp | 0 | 0 | 0 |
|
| pedigreeGrid | 5.19 | 0.00 | 5.19 |
|
| pedigreeViewports | 0.01 | 0.00 | 0.01 |
|