VJ Carey
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) |
| URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools |
| Last Changed Rev: 130496 / Revision: 131943 |
| Last Changed Date: 2017-06-18 11:19:43 -0400 (Sun, 18 Jun 2017) |
| Back to the "Multiple platform build/check report" | A B C D E F [G] H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2017-08-16 13:27:14 -0400 (Wed, 16 Aug 2017).
| Package 567/1410 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| GGtools 5.13.1 VJ Carey
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GGtools |
| Version: 5.13.1 |
| Command: rm -rf GGtools.buildbin-libdir GGtools.Rcheck && mkdir GGtools.buildbin-libdir GGtools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_5.13.1.tar.gz >GGtools.Rcheck\00install.out 2>&1 && cp GGtools.Rcheck\00install.out GGtools-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_5.13.1.tar.gz |
| StartedAt: 2017-08-15 23:50:57 -0400 (Tue, 15 Aug 2017) |
| EndedAt: 2017-08-16 00:07:35 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 998.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GGtools.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf GGtools.buildbin-libdir GGtools.Rcheck && mkdir GGtools.buildbin-libdir GGtools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_5.13.1.tar.gz >GGtools.Rcheck\00install.out 2>&1 && cp GGtools.Rcheck\00install.out GGtools-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_5.13.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '5.13.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'MatrixEQTL'
* 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 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 73.0Mb
sub-directories of 1Mb or more:
data 27.0Mb
doc 1.6Mb
parts 2.0Mb
pup 2.0Mb
rdas 10.3Mb
vcf 28.8Mb
* 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
* 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
'library' or 'require' call to 'Homo.sapiens' which was already attached by Depends.
Please remove these calls from your code.
Namespace in Imports field not imported from: 'stats'
All declared Imports should be used.
Packages in Depends field not imported from:
'Homo.sapiens' 'parallel'
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
.calfig: no visible global function definition for 'axis'
.calfig: no visible global function definition for 'points'
.calfig: no visible global function definition for 'text'
.calfig: no visible global function definition for 'abline'
.summarize: no visible global function definition for 'ftable'
.summarize: no visible binding for global variable 'npc'
.summarize: no visible binding for global variable 'maf'
.summarize: no visible binding for global variable 'radiusUsed'
.summarize: no visible binding for global variable 'excl'
.transTab: no visible global function definition for 'snpsBySeqname'
All.cis.eQTLs: no visible global function definition for 'approx'
SnpMatrixCisToSummex: no visible global function definition for
'rowRanges'
add878: no visible binding for global variable 'hmm878'
add878: no visible global function definition for 'relevel'
addcadd: no visible binding for global variable 'bindcadd'
addcadd: no visible global function definition for '%dopar%'
addcadd: no visible global function definition for 'foreach'
addcadd: no visible binding for global variable 'x'
addgwhit: no visible binding for global variable 'gwastagger'
addgwhit: no visible global function definition for 'overlapsAny'
appraise : <anonymous>: no visible global function definition for
'relevel'
appraise : .redu.fdr: no visible global function definition for
'setkey'
appraise : .redu.fdr: no visible binding for global variable 'snp'
appraise : .redu.fdr: no visible binding for global variable '.N'
appraise : .redu.fdr : <anonymous>: no visible global function
definition for 'setkeyv'
appraise : .redu.fdr : <anonymous>: no visible binding for global
variable '.N'
appraise : .discmods: no visible global function definition for
'%dopar%'
appraise : .discmods: no visible global function definition for
'foreach'
appraise : .discmods: no visible global function definition for
'binomial'
appraise : .discmods: no visible global function definition for
'predict'
appraise : .discmods: no visible global function definition for 'coef'
appraise : .discmods: no visible global function definition for 'vcov'
appraise : .discmods: no visible global function definition for
'model.matrix'
appraise : .discmods: no visible global function definition for
'plogis'
binnedQQ: no visible global function definition for 'par'
binnedQQ: no visible global function definition for 'qqplot'
binnedQQ: no visible global function definition for 'mtext'
binqq: no visible global function definition for 'text'
binqq: no visible global function definition for 'segments'
binqq: no visible global function definition for 'abline'
binqq: no visible global function definition for 'axis'
buildConfList : z : <anonymous>: no visible binding for global variable
'pl'
cgff2dt: no visible global function definition for '%dopar%'
cgff2dt: no visible global function definition for 'foreach'
cgff2dt: no visible global function definition for 'as.data.table'
cgff2dt: no visible binding for global variable 'hmm878'
cgff2dt: no visible global function definition for 'overlapsAny'
cgff2dt: no visible binding for global variable 'gwastagger'
cisAssoc: no visible global function definition for 'rowRanges'
cisAssoc: no visible global function definition for 'assays'
cisAssoc: no visible global function definition for 'as.formula'
cisAssoc: no visible global function definition for 'runif'
cisAssoc: no visible global function definition for 'colData'
cisAssoc: no visible binding for global variable 'chi.squared'
ciseqByCluster : <anonymous>: no visible global function definition for
'detectCores'
ciseqByCluster: no visible binding for '<<-' assignment to 'firstHalf'
ciseqByCluster: no visible binding for '<<-' assignment to 'secondHalf'
ciseqByCluster: no visible binding for '<<-' assignment to 'firstThird'
ciseqByCluster: no visible binding for '<<-' assignment to 'lastThird'
ciseqByCluster: no visible binding for '<<-' assignment to 'midThird'
ciseqByCluster : setupSplit : <anonymous>: no visible binding for
global variable 'mclapply'
ciseqByCluster: no visible binding for '<<-' assignment to
'runOneSplit'
ciseqByCluster : <anonymous>: no visible binding for global variable
'firstHalf'
ciseqByCluster : <anonymous> : cr2gff: no visible global function
definition for 'ranges<-'
ciseqByCluster : <anonymous> : cr2gff: no visible global function
definition for 'export.gff3'
ciseqByCluster: no visible binding for global variable 'firstThird'
ciseqByCluster: no visible binding for global variable 'midThird'
ciseqByCluster: no visible binding for global variable 'lastThird'
ciseqByCluster : <anonymous>: no visible global function definition for
'runOneSplit'
eqBox: no visible global function definition for 'assay'
eqDesc: no visible global function definition for 'assay'
eqsens_dt: no visible global function definition for 'setnames'
eqsens_dt: no visible global function definition for '%dopar%'
eqsens_dt: no visible global function definition for 'foreach'
eqsens_dt: no visible binding for global variable 'curp'
eqtlEstimates : <anonymous>: no visible global function definition for
'formula'
eqtlTests : <anonymous>: no visible global function definition for
'formula'
eqtlTests.me: no visible binding for global variable 'modelLINEAR'
eqtlTests.me: no visible binding for global variable 'SlicedData'
eqtlTests.me: no visible global function definition for 'model.matrix'
eqtlTests.me: no visible binding for global variable
'Matrix_eQTL_engine'
eqtlTests.meText: no visible binding for global variable 'modelLINEAR'
eqtlTests.meText: no visible binding for global variable 'SlicedData'
eqtlTests.meText: no visible binding for global variable
'Matrix_eQTL_engine'
eqtlTests2 : <anonymous>: no visible global function definition for
'formula'
fplot: no visible global function definition for 'forestplot'
genemodel: no visible global function definition for 'select'
genemodel: no visible binding for global variable 'Homo.sapiens'
get.dffits : maxdf: no visible global function definition for 'dffits'
get.dffits : <anonymous>: no visible global function definition for
'lm'
getAsSlicedData: no visible binding for global variable 'target'
getCisMap: no visible global function definition for 'snpsBySeqname'
get_probechunks: no visible global function definition for 'select'
inflammFilter: no visible binding for global variable 'gwrngs'
inflammFilter: no visible global function definition for 'overlapsAny'
makeSeqinfo: no visible binding for global variable 'hg19.si.df'
meqtlTests : gfun: no visible global function definition for 'formula'
pifdr: no visible global function definition for 'hist'
pifdr.old: no visible global function definition for 'approx'
plotsens: no visible binding for global variable 'mafs'
plotsens: no visible binding for global variable 'value'
plotsens: no visible binding for global variable 'FDR'
pullHits: no visible global function definition for 'ranges<-'
qqhex: no visible global function definition for 'qqplot'
richNull : <anonymous>: no visible global function definition for
'bindmaf'
simpleTiling: no visible binding for global variable 'Homo.sapiens'
simpleTiling: no visible global function definition for 'tileGenome'
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
tscan2df: no visible global function definition for '%dopar%'
tscan2df: no visible global function definition for 'foreach'
tscan2df: no visible binding for global variable 'i'
tscan2gr: no visible global function definition for '%dopar%'
tscan2gr: no visible global function definition for 'foreach'
tscan2gr: no visible binding for global variable 'i'
waldtests : <anonymous>: no visible global function definition for
'wald.test'
plot,gwSnpScreenResult-character: no visible global function definition
for 'snpcount'
plot,gwSnpScreenResult-character: no visible global function definition
for 'snpsBySeqname'
plot,gwSnpScreenResult-character: no visible global function definition
for 'pos'
plot,gwSnpScreenResult-character: no visible binding for global
variable 'smoothScatter'
plot,gwSnpScreenResult-character: no visible global function definition
for 'axis'
Undefined global functions or variables:
%dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData abline
approx as.data.table as.formula assay assays axis bindcadd bindmaf
binomial chi.squared coef colData curp detectCores dffits excl
export.gff3 firstHalf firstThird foreach forestplot formula ftable
gwastagger gwrngs hg19.si.df hist hmm878 i i1 i2 lastThird lm maf
mafs mclapply midThird model.matrix modelLINEAR mtext npc overlapsAny
par pl plogis points pos predict qqplot radiusUsed ranges<- relevel
rowRanges runOneSplit runif segments select setkey setkeyv setnames
smoothScatter snp snpcount snpsBySeqname target text tileGenome value
vcov wald.test x
Consider adding
importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
"points", "segments", "smoothScatter", "text")
importFrom("stats", "approx", "as.formula", "binomial", "coef",
"dffits", "formula", "ftable", "lm", "model.matrix",
"plogis", "predict", "qqplot", "relevel", "runif", "vcov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'MatrixEQTL'
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
cisAssoc 41.47 1.64 43.11
eqtlTests 7.64 0.40 8.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cisAssoc 59.51 2.80 62.38
eqtlTests 9.23 0.46 9.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'cis.R'
Running 'eqvgwst.R'
Running 'test.meqtlTests.R'
Running 'test.meta.trans.R'
Running 'testCisMap.R'
Running 'testTrans.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/R" CMD BATCH --vanilla "testTrans.R" "testTrans.Rout"' had status 1
ERROR
Running the tests in 'tests/testTrans.R' failed.
Last 13 lines of output:
> tt1 = transTab(t1)
Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh37
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Error: cannot allocate vector of size 2.0 Gb
Execution halted
** running tests for arch 'x64' ...
Running 'cis.R'
Running 'eqvgwst.R'
Running 'test.meqtlTests.R'
Running 'test.meta.trans.R'
Running 'testCisMap.R'
Running 'testTrans.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 ERROR, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/00check.log'
for details.
testTrans.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # verifies that transScores agrees with snp.rhs.tests to obtain best
> # trans scores
>
> suppressPackageStartupMessages(library(GGtools))
No methods found in "RSQLite" for requests: dbGetQuery
>
> tenOn2021 =
+ c( "GI_4557248-S", "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+ "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S")
>
> tconf = new("TransConfig")
> radius(tconf) = 2000000L
> smpack(tconf) = "GGdata"
> rhs(tconf) = ˜1
> snpchr(tconf) = "22" # we get scores for all SNP on this chrom
> chrnames(tconf) = c("20", "21")
> gbufsize(tconf) = 4L
> smFilter(tconf) = function(x) x[probeId(tenOn2021),]
> snpannopk(tconf) = snplocsDefault()
> schrpref(tconf) = "ch"
> exFilter(tconf) = function(x)x
> gchrpref = ""
> batchsize(tconf) = 200L
>
> suppressPackageStartupMessages(library(GGtools))
>
> t1 = transScores(tconf)
Loading required package: illuminaHumanv1.db
opening ff C:/Users/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsc_20_chr22.ff
2opening ff C:/Users/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsctmp2_chr22.ff
>
> #"GGdata", rhs=˜1, snpchr="22", chrnames=as.character(c(20,21)),
> #
> # all tests are trans, to verify buffering approach
> #
> # radius = 2e+06, K=4,
> # probesToKeep = tenOn2021, batchsize = 200,
> # geneannopk = "illuminaHumanv1.db",
> # snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "",
> # schrpref = "ch", exFilter = function(x) x)
>
> tt1 = transTab(t1)
Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh37
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Error: cannot allocate vector of size 2.0 Gb
Execution halted
GGtools.Rcheck/00install.out:
install for i386 * installing *source* package 'GGtools' ... ** R ** data ** inst ** preparing package for lazy loading No methods found in "RSQLite" for requests: dbGetQuery ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in "RSQLite" for requests: dbGetQuery install for x64 * installing *source* package 'GGtools' ... ** testing if installed package can be loaded No methods found in "RSQLite" for requests: dbGetQuery * MD5 sums packaged installation of 'GGtools' as GGtools_5.13.1.zip * DONE (GGtools)
GGtools.Rcheck/examples_i386/GGtools-Ex.timings:
| name | user | system | elapsed | |
| All.cis | 0 | 0 | 0 | |
| CisConfig-class | 0 | 0 | 0 | |
| EqAppr-class | 0 | 0 | 0 | |
| GGtools-package | 0 | 0 | 0 | |
| TransConfig-class | 0 | 0 | 0 | |
| b1 | 0.08 | 0.01 | 0.09 | |
| best.cis.eQTLs | 0 | 0 | 0 | |
| best.trans.eQTLs | 0 | 0 | 0 | |
| bindmaf | 0 | 0 | 0 | |
| cgff2dt | 0.01 | 0.00 | 0.02 | |
| cisAssoc | 41.47 | 1.64 | 43.11 | |
| cisRun-class | 0 | 0 | 0 | |
| ciseqByCluster | 0 | 0 | 0 | |
| collectBest | 0 | 0 | 0 | |
| concatCis | 0 | 0 | 0 | |
| eqBox | 2.22 | 0.10 | 2.31 | |
| eqsens_dt | 0 | 0 | 0 | |
| eqtlTests | 7.64 | 0.40 | 8.25 | |
| eqtlTests.me | 0 | 0 | 0 | |
| eqtlTestsManager-class | 0 | 0 | 0 | |
| ex | 2.67 | 0.05 | 2.72 | |
| getCisMap | 0 | 0 | 0 | |
| gwSnpTests | 3.37 | 0.07 | 3.46 | |
| hmm878 | 0.61 | 0.05 | 0.65 | |
| pifdr | 1.35 | 0.02 | 1.36 | |
| qqhex | 0.09 | 0.01 | 0.11 | |
| sampsInVCF | 0.03 | 0.00 | 0.03 | |
| sensiCisInput-class | 0 | 0 | 0 | |
| sensiCisOutput-class | 0 | 0 | 0 | |
| simpleTiling | 0 | 0 | 0 | |
| snplocsDefault | 0 | 0 | 0 | |
| strMultPop | 0.08 | 0.00 | 0.08 | |
| transManager-class | 0 | 0 | 0 | |
| transScores | 0 | 0 | 0 | |
| vcf2sm | 0.06 | 0.00 | 0.06 | |
GGtools.Rcheck/examples_x64/GGtools-Ex.timings:
| name | user | system | elapsed | |
| All.cis | 0 | 0 | 0 | |
| CisConfig-class | 0 | 0 | 0 | |
| EqAppr-class | 0 | 0 | 0 | |
| GGtools-package | 0 | 0 | 0 | |
| TransConfig-class | 0 | 0 | 0 | |
| b1 | 0.33 | 0.00 | 0.33 | |
| best.cis.eQTLs | 0 | 0 | 0 | |
| best.trans.eQTLs | 0 | 0 | 0 | |
| bindmaf | 0 | 0 | 0 | |
| cgff2dt | 0.02 | 0.00 | 0.01 | |
| cisAssoc | 59.51 | 2.80 | 62.38 | |
| cisRun-class | 0 | 0 | 0 | |
| ciseqByCluster | 0 | 0 | 0 | |
| collectBest | 0 | 0 | 0 | |
| concatCis | 0 | 0 | 0 | |
| eqBox | 3.39 | 0.21 | 3.61 | |
| eqsens_dt | 0 | 0 | 0 | |
| eqtlTests | 9.23 | 0.46 | 9.80 | |
| eqtlTests.me | 0 | 0 | 0 | |
| eqtlTestsManager-class | 0 | 0 | 0 | |
| ex | 2.63 | 0.09 | 2.72 | |
| getCisMap | 0 | 0 | 0 | |
| gwSnpTests | 3.58 | 0.08 | 3.66 | |
| hmm878 | 0.53 | 0.09 | 0.62 | |
| pifdr | 1.66 | 0.00 | 1.66 | |
| qqhex | 0.11 | 0.00 | 0.11 | |
| sampsInVCF | 0.05 | 0.00 | 0.05 | |
| sensiCisInput-class | 0 | 0 | 0 | |
| sensiCisOutput-class | 0 | 0 | 0 | |
| simpleTiling | 0.01 | 0.00 | 0.01 | |
| snplocsDefault | 0 | 0 | 0 | |
| strMultPop | 0.08 | 0.00 | 0.08 | |
| transManager-class | 0 | 0 | 0 | |
| transScores | 0 | 0 | 0 | |
| vcf2sm | 0.09 | 0.00 | 0.09 | |