BioC 3.3: CHECK report for gwascat on windows2.bioconductor.org
This page was generated on 2015-10-27 12:14:58 -0400 (Tue, 27 Oct 2015).
gwascat 2.3.0
VJ Carey
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gwascat | | 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 | OK | OK | ERROR | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK | |
Summary
| Package: gwascat
|
| Version: 2.3.0
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| Command: rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.3.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.3.0.tar.gz
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| StartedAt: 2015-10-27 03:08:54 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 03:16:41 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 467.5 seconds
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| RetCode: 1
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| Status: ERROR
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| CheckDir: gwascat.Rcheck
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| Warnings: NA
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Command output
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###
### Running command:
###
### rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.3.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.3.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/gwascat.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 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.3.0'
* 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 'gwascat' can be installed ... OK
* checking installed package size ... NOTE
installed size is 38.6Mb
sub-directories of 1Mb or more:
data 30.8Mb
obo 3.0Mb
olddata 2.2Mb
tab 1.1Mb
* 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
Namespace in Imports field not imported from: 'VariantAnnotation'
All declared Imports should be used.
Package in Depends field not imported from: 'Homo.sapiens'
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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindcadd_snv: no visible global function definition for 'findOverlaps'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'getSNPlocs'
gwcex2gviz: no visible global function definition for 'mapIds'
ldtagr: no visible global function definition for 'rowRanges'
ldtagr: no visible global function definition for 'col.summary'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat.legacy: no visible binding for global variable
'si.hs.38'
snpGenos: no visible global function definition for 'getSNPlocs'
tfilt: no visible binding for global variable 'phr'
tpad: no visible binding for global variable 'phr'
traitsManh: no visible binding for global variable 'PVALUE_MLOG'
variantProps: no visible binding for global variable 'gwrngs'
Undefined global functions or variables:
PVALUE_MLOG col.summary findOverlaps getSNPlocs gwrngs gwrngs19
mapIds phr rowRanges si.hs.37 si.hs.38
* 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' ... [33s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 10.92 0.04 10.97
gwcex2gviz 5.08 0.35 5.42
** running examples for arch 'x64' ... [36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 13.32 0.08 13.41
gwcex2gviz 5.37 0.19 5.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R' [13s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-B/R/bin/i386/R" CMD BATCH --vanilla "test-all.R" "test-all.Rout"' had status 1
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
ERROR in c:/biocbld/bbs-3.3-bioc/meat/gwascat.buildbin-libdir/gwascat/unitTests/test_gwascat.R: Error while sourcing c:/biocbld/bbs-3.3-bioc/meat/gwascat.buildbin-libdir/gwascat/unitTests/test_gwascat.R : Error in checkTrue(identical(topTraits(ebicat38), tt38saved)) :
Test not TRUE
Test files with failing tests
test_gwascat.R
c:/biocbld/bbs-3.3-bioc/meat/gwascat.buildbin-libdir/gwascat/unitTests/test_gwascat.R
Error in BiocGenerics:::testPackage("gwascat") :
unit tests failed for package gwascat
Execution halted
** running tests for arch 'x64' ...
Running 'test-all.R' [15s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-B/R/bin/x64/R" CMD BATCH --vanilla "test-all.R" "test-all.Rout"' had status 1
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
ERROR in c:/biocbld/bbs-3.3-bioc/meat/gwascat.buildbin-libdir/gwascat/unitTests/test_gwascat.R: Error while sourcing c:/biocbld/bbs-3.3-bioc/meat/gwascat.buildbin-libdir/gwascat/unitTests/test_gwascat.R : Error in checkTrue(identical(topTraits(ebicat38), tt38saved)) :
Test not TRUE
Test files with failing tests
test_gwascat.R
c:/biocbld/bbs-3.3-bioc/meat/gwascat.buildbin-libdir/gwascat/unitTests/test_gwascat.R
Error in BiocGenerics:::testPackage("gwascat") :
unit tests failed for package gwascat
Execution halted
* 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 ERRORs, 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/gwascat.Rcheck/00check.log'
for details.
gwascat.Rcheck/00install.out:
install for i386
* installing *source* package 'gwascat' ...
** R
** data
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
install for x64
* installing *source* package 'gwascat' ...
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* MD5 sums
packaged installation of 'gwascat' as gwascat_2.3.0.zip
* DONE (gwascat)
gwascat.Rcheck/examples_i386/gwascat-Ex.timings:
| name | user | system | elapsed
|
| bindcadd_snv | 0 | 0 | 0 |
|
| gwascat-package | 0 | 0 | 0 |
|
| gwastagger | 1.62 | 0.03 | 1.65 |
|
| gwaswloc-class | 0.34 | 0.00 | 0.34 |
|
| gwcex2gviz | 5.08 | 0.35 | 5.42 |
|
| gwdf_2012_02_02 | 0 | 0 | 0 |
|
| ldtagr | 0.38 | 0.14 | 0.52 |
|
| locon6 | 0.03 | 0.00 | 0.03 |
|
| makeCurrentGwascat | 0 | 0 | 0 |
|
| obo2graphNEL | 0.19 | 0.05 | 0.23 |
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| riskyAlleleCount | 10.92 | 0.04 | 10.97 |
|
| topTraits | 0.33 | 0.00 | 0.33 |
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| traitsManh | 0.72 | 0.00 | 0.72 |
|
gwascat.Rcheck/examples_x64/gwascat-Ex.timings:
| name | user | system | elapsed
|
| bindcadd_snv | 0 | 0 | 0 |
|
| gwascat-package | 0 | 0 | 0 |
|
| gwastagger | 1.94 | 0.05 | 1.98 |
|
| gwaswloc-class | 0 | 0 | 0 |
|
| gwcex2gviz | 5.37 | 0.19 | 5.56 |
|
| gwdf_2012_02_02 | 0 | 0 | 0 |
|
| ldtagr | 0.47 | 0.01 | 0.49 |
|
| locon6 | 0.03 | 0.00 | 0.03 |
|
| makeCurrentGwascat | 0 | 0 | 0 |
|
| obo2graphNEL | 0.35 | 0.00 | 0.34 |
|
| riskyAlleleCount | 13.32 | 0.08 | 13.41 |
|
| topTraits | 0.29 | 0.00 | 0.28 |
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| traitsManh | 0.79 | 0.00 | 0.80 |
|