BioC 3.3: CHECK report for bioassayR on moscato2
This page was generated on 2016-10-13 12:51:56 -0700 (Thu, 13 Oct 2016).
bioassayR 1.10.15
Tyler Backman
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/bioassayR | | Last Changed Rev: 119996 / Revision: 122332 | | Last Changed Date: 2016-08-09 09:20:48 -0700 (Tue, 09 Aug 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: bioassayR
|
| Version: 1.10.15
|
| Command: rm -rf bioassayR.buildbin-libdir bioassayR.Rcheck && mkdir bioassayR.buildbin-libdir bioassayR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bioassayR.buildbin-libdir bioassayR_1.10.15.tar.gz >bioassayR.Rcheck\00install.out 2>&1 && cp bioassayR.Rcheck\00install.out bioassayR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=bioassayR.buildbin-libdir --install="check:bioassayR-install.out" --force-multiarch --no-vignettes --timings bioassayR_1.10.15.tar.gz
|
| StartedAt: 2016-10-13 01:22:11 -0700 (Thu, 13 Oct 2016)
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| EndedAt: 2016-10-13 01:24:49 -0700 (Thu, 13 Oct 2016)
|
| EllapsedTime: 158.3 seconds
|
| RetCode: 0
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| Status: OK
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| CheckDir: bioassayR.Rcheck
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| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf bioassayR.buildbin-libdir bioassayR.Rcheck && mkdir bioassayR.buildbin-libdir bioassayR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bioassayR.buildbin-libdir bioassayR_1.10.15.tar.gz >bioassayR.Rcheck\00install.out 2>&1 && cp bioassayR.Rcheck\00install.out bioassayR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=bioassayR.buildbin-libdir --install="check:bioassayR-install.out" --force-multiarch --no-vignettes --timings bioassayR_1.10.15.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/bioassayR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bioassayR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bioassayR' version '1.10.15'
* 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 'bioassayR' 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
** 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
crossReactivityPrior: no visible global function definition for 'sd'
crossReactivityProbability : <anonymous>: no visible global function
definition for 'pbeta'
Undefined global functions or variables:
pbeta sd
Consider adding
importFrom("stats", "pbeta", "sd")
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 installed files from 'inst/doc' ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 1 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/bioassayR.Rcheck/00check.log'
for details.
bioassayR.Rcheck/00install.out:
install for i386
* installing *source* package 'bioassayR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'organism' in package 'bioassayR'
Creating a new generic function for 'organism<-' in package 'bioassayR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'bioassayR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bioassayR' as bioassayR_1.10.15.zip
* DONE (bioassayR)
bioassayR.Rcheck/examples_i386/bioassayR-Ex.timings:
| name | user | system | elapsed
|
| BioAssayDB-class | 0 | 0 | 0 |
|
| activeAgainst | 0.01 | 0.00 | 0.02 |
|
| activeTargets | 0.02 | 0.00 | 0.02 |
|
| addBioassayIndex | 0.01 | 0.00 | 0.01 |
|
| addDataSource | 0.02 | 0.00 | 0.02 |
|
| allCids | 0 | 0 | 0 |
|
| allTargets | 0.01 | 0.00 | 0.01 |
|
| assaySetTargets | 0.04 | 0.00 | 0.03 |
|
| bioactivityFingerprint | 0.31 | 0.00 | 0.32 |
|
| bioassay-class | 0.03 | 0.00 | 0.03 |
|
| bioassaySet-class | 0 | 0 | 0 |
|
| connectBioassayDB | 0.01 | 0.00 | 0.01 |
|
| crossReactivityProbability | 0.28 | 0.01 | 0.30 |
|
| disconnectBioassayDB | 0.02 | 0.00 | 0.01 |
|
| dropBioassay | 0.03 | 0.02 | 0.35 |
|
| dropBioassayIndex | 0.02 | 0.00 | 0.01 |
|
| getAssay | 0.01 | 0.00 | 0.02 |
|
| getAssays | 0.02 | 0.00 | 0.01 |
|
| getBioassaySetByCids | 0.26 | 0.00 | 0.27 |
|
| inactiveTargets | 0.02 | 0.00 | 0.01 |
|
| loadBioassay | 0.03 | 0.00 | 0.04 |
|
| loadIdMapping | 0.02 | 0.00 | 0.01 |
|
| newBioassayDB | 0 | 0 | 0 |
|
| parsePubChemBioassay | 0 | 0 | 0 |
|
| perTargetMatrix | 0.28 | 0.00 | 0.28 |
|
| queryBioassayDB | 0.00 | 0.01 | 0.01 |
|
| samplebioassay | 0 | 0 | 0 |
|
| scaleBioassaySet | 0.03 | 0.00 | 0.04 |
|
| screenedAtLeast | 0.01 | 0.00 | 0.01 |
|
| selectiveAgainst | 0.13 | 0.02 | 0.14 |
|
| targetSelectivity | 0.03 | 0.00 | 0.03 |
|
| translateTargetId | 0.02 | 0.00 | 0.02 |
|
| trinarySimilarity | 0.32 | 0.00 | 0.33 |
|
bioassayR.Rcheck/examples_x64/bioassayR-Ex.timings:
| name | user | system | elapsed
|
| BioAssayDB-class | 0 | 0 | 0 |
|
| activeAgainst | 0 | 0 | 0 |
|
| activeTargets | 0.02 | 0.00 | 0.01 |
|
| addBioassayIndex | 0.01 | 0.00 | 0.02 |
|
| addDataSource | 0.04 | 0.00 | 0.03 |
|
| allCids | 0 | 0 | 0 |
|
| allTargets | 0.01 | 0.00 | 0.02 |
|
| assaySetTargets | 0.05 | 0.00 | 0.04 |
|
| bioactivityFingerprint | 0.29 | 0.00 | 0.30 |
|
| bioassay-class | 0.00 | 0.02 | 0.02 |
|
| bioassaySet-class | 0.02 | 0.00 | 0.01 |
|
| connectBioassayDB | 0 | 0 | 0 |
|
| crossReactivityProbability | 0.28 | 0.00 | 0.28 |
|
| disconnectBioassayDB | 0.01 | 0.00 | 0.01 |
|
| dropBioassay | 0.06 | 0.00 | 0.63 |
|
| dropBioassayIndex | 0.04 | 0.00 | 0.03 |
|
| getAssay | 0 | 0 | 0 |
|
| getAssays | 0.03 | 0.00 | 0.03 |
|
| getBioassaySetByCids | 0.28 | 0.00 | 0.28 |
|
| inactiveTargets | 0.01 | 0.00 | 0.02 |
|
| loadBioassay | 0.07 | 0.00 | 0.06 |
|
| loadIdMapping | 0.01 | 0.00 | 0.01 |
|
| newBioassayDB | 0.02 | 0.00 | 0.02 |
|
| parsePubChemBioassay | 0.01 | 0.00 | 0.01 |
|
| perTargetMatrix | 0.49 | 0.00 | 0.49 |
|
| queryBioassayDB | 0.03 | 0.00 | 0.03 |
|
| samplebioassay | 0 | 0 | 0 |
|
| scaleBioassaySet | 0.04 | 0.00 | 0.04 |
|
| screenedAtLeast | 0.02 | 0.00 | 0.02 |
|
| selectiveAgainst | 0.2 | 0.0 | 0.2 |
|
| targetSelectivity | 0.03 | 0.00 | 0.03 |
|
| translateTargetId | 0.02 | 0.00 | 0.02 |
|
| trinarySimilarity | 0.47 | 0.00 | 0.47 |
|