Christian Arnold
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SNPhood |
| Branch: RELEASE_3_10 |
| Last Commit: 545f6a7 |
| Last Changed Date: 2019-10-29 13:09:29 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:41 -0400 (Wed, 15 Apr 2020).
| Package 1625/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SNPhood 1.16.0 Christian Arnold
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SNPhood |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPhood.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SNPhood_1.16.0.tar.gz |
| StartedAt: 2020-04-15 06:45:57 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:01:54 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 956.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SNPhood.Rcheck |
| Warnings: 1 |
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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:SNPhood.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SNPhood_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SNPhood.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 'SNPhood/DESCRIPTION' ... OK
* this is package 'SNPhood' version '1.16.0'
* 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 'SNPhood' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpkpyecT/R.INSTALL206c7b1241a2/SNPhood/man/collectFiles.Rd:46: file link 'path' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SNPhood.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
not specified by mailto: nor contained in < >
use the Contact field instead
* 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
.calcBinomTestVector: no visible binding for global variable 'pp'
Undefined global functions or variables:
pp
* 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
analyzeSNPhood 70.56 3.14 112.43
testForAllelicBiases 26.36 0.72 27.60
plotAllelicBiasResults 23.80 0.70 25.28
plotFDRResults 21.89 1.09 23.55
plotAndSummarizeAllelicBiasTest 21.44 1.09 23.48
results 4.90 2.20 7.11
associateGenotypes 6.55 0.02 6.58
plotRegionCounts 2.83 0.17 6.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeSNPhood 91.11 5.06 103.16
plotAllelicBiasResults 27.09 0.27 28.15
plotAndSummarizeAllelicBiasTest 23.09 0.25 25.05
testForAllelicBiases 22.30 0.25 22.94
plotFDRResults 21.38 0.30 27.17
results 4.91 2.55 7.45
associateGenotypes 5.99 0.06 6.05
plotRegionCounts 3.64 0.17 11.31
plotAllelicBiasResultsOverview 2.67 0.08 5.05
annotationBins2 1.61 0.02 5.02
* 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/SNPhood.Rcheck/00check.log'
for details.
SNPhood.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/SNPhood_1.16.0.tar.gz && rm -rf SNPhood.buildbin-libdir && mkdir SNPhood.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPhood.buildbin-libdir SNPhood_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SNPhood_1.16.0.zip && rm SNPhood_1.16.0.tar.gz SNPhood_1.16.0.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
54 3966k 54 2176k 0 0 4130k 0 --:--:-- --:--:-- --:--:-- 4152k
100 3966k 100 3966k 0 0 5618k 0 --:--:-- --:--:-- --:--:-- 5642k
install for i386
* installing *source* package 'SNPhood' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SNPhood'
finding HTML links ... done
SNPhood-class html
SNPhood html
SNPhood.o html
analyzeSNPhood html
finding level-2 HTML links ... done
annotation-methods html
annotationBins html
annotationBins2 html
annotationDatasets html
annotationReadGroups html
annotationRegions html
associateGenotypes html
bins-methods html
changeObjectIntegrityChecking html
collectFiles html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpkpyecT/R.INSTALL206c7b1241a2/SNPhood/man/collectFiles.Rd:46: file link 'path' in package 'Rsamtools' does not exist and so has been treated as a topic
convertToAllelicFractions html
counts-method html
datasets-methods html
deleteDatasets html
deleteReadGroups html
deleteRegions html
enrichment-methods html
getDefaultParameterList html
mergeReadGroups html
parameters-methods html
plotAllelicBiasResults html
plotAllelicBiasResultsOverview html
plotAndCalculateCorrelationDatasets html
plotAndCalculateWeakAndStrongGenotype html
plotAndClusterMatrix html
plotAndSummarizeAllelicBiasTest html
plotBinCounts html
plotClusterAverage html
plotFDRResults html
plotGenotypesPerCluster html
plotGenotypesPerSNP html
plotRegionCounts html
readGroups-methods html
regions-methods html
renameBins html
renameDatasets html
renameReadGroups html
renameRegions html
results html
testForAllelicBiases 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 'SNPhood' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPhood' as SNPhood_1.16.0.zip
* DONE (SNPhood)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SNPhood' successfully unpacked and MD5 sums checked
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SNPhood.Rcheck/examples_i386/SNPhood-Ex.timings
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SNPhood.Rcheck/examples_x64/SNPhood-Ex.timings
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