BioC 3.2: CHECK report for gQTLstats on windows1.bioconductor.org
This page was generated on 2015-10-27 17:31:52 -0400 (Tue, 27 Oct 2015).
gQTLstats 1.2.0
VJ Carey
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/gQTLstats | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: gQTLstats
|
| Version: 1.2.0
|
| Command: rm -rf gQTLstats.buildbin-libdir gQTLstats.Rcheck && mkdir gQTLstats.buildbin-libdir gQTLstats.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLstats.buildbin-libdir gQTLstats_1.2.0.tar.gz >gQTLstats.Rcheck\00install.out 2>&1 && cp gQTLstats.Rcheck\00install.out gQTLstats-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gQTLstats.buildbin-libdir --install="check:gQTLstats-install.out" --force-multiarch --no-vignettes --timings gQTLstats_1.2.0.tar.gz
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| StartedAt: 2015-10-27 02:27:03 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 02:49:57 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 1373.6 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: gQTLstats.Rcheck
|
| Warnings: 0
|
Command output
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### Running command:
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### rm -rf gQTLstats.buildbin-libdir gQTLstats.Rcheck && mkdir gQTLstats.buildbin-libdir gQTLstats.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLstats.buildbin-libdir gQTLstats_1.2.0.tar.gz >gQTLstats.Rcheck\00install.out 2>&1 && cp gQTLstats.Rcheck\00install.out gQTLstats-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gQTLstats.buildbin-libdir --install="check:gQTLstats-install.out" --force-multiarch --no-vignettes --timings gQTLstats_1.2.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/gQTLstats.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gQTLstats/DESCRIPTION' ... OK
* this is package 'gQTLstats' version '1.2.0'
* 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 'gQTLstats' can be installed ... OK
* checking installed package size ... NOTE
installed size is 16.6Mb
sub-directories of 1Mb or more:
data 9.6Mb
vcf 5.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.eqBox: no visible global function definition for
'SnpMatrixCisToSummex'
.eqDesc: no visible global function definition for
'SnpMatrixCisToSummex'
cisAssoc: no visible global function definition for 'DNAStringSetList'
cisCount: no visible global function definition for 'DNAStringSetList'
gmod2: no visible binding for global variable 'Homo.sapiens'
gmod2: no visible binding for global variable 'exonsBy'
manhWngr: no visible binding for global variable 'ml10fdr'
maxByFeature: no visible binding for global variable 'snp'
maxByFeature: no visible binding for global variable 'chisq'
maxByFeature: no visible binding for global variable 'probeid'
maxByProbeOLD: no visible binding for global variable 'snp'
maxByProbeOLD: no visible binding for global variable 'probeid'
maxByProbeOLD: no visible binding for global variable 'chisq'
maxByProbeOLD: no visible binding for global variable 'permScore_1'
maxByProbeOLD: no visible binding for global variable 'permScore_2'
maxByProbeOLD: no visible binding for global variable 'permScore_3'
plot.senstab: no visible binding for global variable 'MAF'
plot.senstab: no visible binding for global variable 'value'
plot.senstab: no visible binding for global variable 'criterion'
plot.table.sensobj: no visible binding for global variable 'maf'
plot.table.sensobj: no visible binding for global variable 'calls'
prep.cisAssocNB: no visible global function definition for
'DNAStringSetList'
storeToHist: no visible binding for global variable 'x'
storeToMaxAssocBySNP: no visible binding for global variable 'snp'
storeToMaxAssocBySNP: no visible binding for global variable 'chisq'
storeToMaxAssocBySNP: no visible binding for global variable
'permScore_1'
storeToMaxAssocBySNP: no visible binding for global variable
'permScore_2'
storeToMaxAssocBySNP: no visible binding for global variable
'permScore_3'
storeToMaxAssocBySNP: no visible global function definition for 'nth'
storeToMaxAssocBySNP: no visible binding for global variable 'MAF'
storeToMaxAssocBySNP: no visible binding for global variable 'probeid'
storeToMaxAssocBySNP: no visible binding for global variable 'mindist'
* 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 ... NOTE
Note: found 8 marked Latin-1 strings
Note: found 8 marked UTF-8 strings
* 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' ... [306s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeToStats 158.99 3.10 168.53
enumerateByFDR 46.81 2.02 50.59
clipPCs 37.00 0.81 37.81
cisAssoc 11.27 0.39 11.71
eqBox2 9.91 0.29 10.72
queryVCF 9.60 0.11 9.70
** running examples for arch 'x64' ... [278s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeToStats 142.30 2.60 145.00
enumerateByFDR 46.14 2.32 48.50
clipPCs 35.19 1.13 36.31
cisAssoc 10.59 0.22 10.83
queryVCF 9.47 0.25 9.72
eqBox2 8.36 0.25 8.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R' [250s]
[250s] OK
** running tests for arch 'x64' ...
Running 'test-all.R' [235s]
[236s] 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: 3 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/gQTLstats.Rcheck/00check.log'
for details.
gQTLstats.Rcheck/00install.out:
install for i386
* installing *source* package 'gQTLstats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'gQTLstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLstats' as gQTLstats_1.2.0.zip
* DONE (gQTLstats)
gQTLstats.Rcheck/examples_i386/gQTLstats-Ex.timings:
| name | user | system | elapsed
|
| FDRsupp-class | 0 | 0 | 0 |
|
| cisAssoc | 11.27 | 0.39 | 11.71 |
|
| clipPCs | 37.00 | 0.81 | 37.81 |
|
| directPlot | 0.03 | 0.00 | 0.04 |
|
| enumerateByFDR | 46.81 | 2.02 | 50.59 |
|
| eqBox2 | 9.91 | 0.29 | 10.72 |
|
| filtFDR | 0.02 | 0.00 | 0.02 |
|
| hmm878 | 0.92 | 0.05 | 0.97 |
|
| manhWngr | 4.36 | 0.17 | 4.55 |
|
| queryVCF | 9.60 | 0.11 | 9.70 |
|
| senstab | 1.11 | 0.00 | 1.11 |
|
| setFDRfunc | 0.03 | 0.00 | 0.03 |
|
| storeToStats | 158.99 | 3.10 | 168.53 |
|
| txsPlot | 0.04 | 0.00 | 0.03 |
|
gQTLstats.Rcheck/examples_x64/gQTLstats-Ex.timings:
| name | user | system | elapsed
|
| FDRsupp-class | 0 | 0 | 0 |
|
| cisAssoc | 10.59 | 0.22 | 10.83 |
|
| clipPCs | 35.19 | 1.13 | 36.31 |
|
| directPlot | 0.02 | 0.00 | 0.03 |
|
| enumerateByFDR | 46.14 | 2.32 | 48.50 |
|
| eqBox2 | 8.36 | 0.25 | 8.61 |
|
| filtFDR | 0.01 | 0.02 | 0.03 |
|
| hmm878 | 0.71 | 0.03 | 0.74 |
|
| manhWngr | 3.39 | 0.13 | 3.51 |
|
| queryVCF | 9.47 | 0.25 | 9.72 |
|
| senstab | 1.17 | 0.01 | 1.19 |
|
| setFDRfunc | 0.01 | 0.00 | 0.01 |
|
| storeToStats | 142.3 | 2.6 | 145.0 |
|
| txsPlot | 0.03 | 0.00 | 0.03 |
|