VJ Carey
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/gQTLstats |
| Branch: RELEASE_3_11 |
| Last Commit: 76f19c8 |
| Last Changed Date: 2020-04-27 14:45:48 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:45 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE gQTLstats PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 768/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gQTLstats 1.20.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: gQTLstats |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gQTLstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gQTLstats_1.20.0.tar.gz |
| StartedAt: 2020-10-17 04:40:48 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:15:00 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 2052.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gQTLstats.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gQTLstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gQTLstats_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gQTLstats.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.20.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo3WcQB/R.INSTALLc904cd26352/gQTLstats/man/TransStore.Rd:18: file link 'Registry' in package 'BatchJobs' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gQTLstats.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 64.4Mb
sub-directories of 1Mb or more:
data 11.0Mb
registries 18.5Mb
vcf 33.8Mb
* 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
TransStore: no visible binding for global variable 'i'
TransStore : <anonymous>: no visible binding for global variable 'i'
cisAssoc: no visible global function definition for 'DNAStringSetList'
cisCount: no visible global function definition for 'DNAStringSetList'
cisEsts: no visible global function definition for 'DNAStringSetList'
eqBox4: no visible binding for global variable 'gt'
eqBox4: no visible binding for global variable 'ex'
eqBox4: no visible binding for global variable 'id'
eqBox4: no visible global function definition for 'geom_boxplot'
gQTLs: no visible binding for global variable 'ch'
gmod2: no visible binding for global variable 'exonsBy'
gmod2: no visible global function definition for 'TxDb'
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'
setFDRfunc: no visible binding for global variable 'assoc'
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'
tqbrowser: no visible global function definition for 'experiments'
tqbrowser : server: no visible global function definition for
'experiments'
tqbrowser : server: no visible global function definition for
'TabixFile'
tqbrowser : server: no visible binding for global variable 'assoc'
tqbrowser : server: no visible binding for global variable 'stateid'
tqbrowser : server: no visible binding for global variable 'state'
transTable: no visible binding for global variable 'i'
tsByRank_sing: no visible binding for global variable 'i'
tsByRank_sing : <anonymous>: no visible binding for global variable 'i'
boxswarm,SnpToGeneQTL: no visible binding for global variable 'g1'
Undefined global functions or variables:
DNAStringSetList MAF TabixFile TxDb assoc calls ch chisq criterion ex
exonsBy experiments g1 geom_boxplot gt i id maf mindist ml10fdr nth
permScore_1 permScore_2 permScore_3 probeid snp state stateid value x
* 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 ... NOTE
Output for data("bigfiltFDR", package = "gQTLstats"):
Output for data("bigrawFDR", package = "gQTLstats"):
Output for data("filtFDR", package = "gQTLstats"):
Output for data("rawFDR", package = "gQTLstats"):
Output for data("sensByProbe", package = "gQTLstats"):
* checking data for non-ASCII characters ... NOTE
Note: found 8 marked Latin-1 strings
Note: found 12 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clipPCs 59.36 1.13 60.50
cisAssoc 34.45 2.25 46.90
gQTLs 14.58 0.33 14.90
eqBox2 14.04 0.30 14.33
queryVCF 12.50 0.34 13.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clipPCs 50.93 1.26 52.23
cisAssoc 24.87 0.75 27.70
eqBox2 11.38 0.12 11.50
gQTLs 10.62 0.30 10.92
queryVCF 8.26 0.15 8.44
manhWngr 3.07 0.32 38.81
setFDRfunc 0.08 0.00 7.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.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 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/gQTLstats.Rcheck/00check.log'
for details.
gQTLstats.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/gQTLstats_1.20.0.tar.gz && rm -rf gQTLstats.buildbin-libdir && mkdir gQTLstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gQTLstats.buildbin-libdir gQTLstats_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gQTLstats_1.20.0.zip && rm gQTLstats_1.20.0.tar.gz gQTLstats_1.20.0.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
3 62.6M 3 2288k 0 0 4863k 0 0:00:13 --:--:-- 0:00:13 4920k
57 62.6M 57 36.2M 0 0 23.5M 0 0:00:02 0:00:01 0:00:01 23.6M
84 62.6M 84 52.9M 0 0 21.4M 0 0:00:02 0:00:02 --:--:-- 21.4M
100 62.6M 100 62.6M 0 0 22.4M 0 0:00:02 0:00:02 --:--:-- 22.4M
install for i386
* installing *source* package 'gQTLstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gQTLstats'
finding HTML links ... done
FDRsupp-class html
TransStore-class html
finding level-2 HTML links ... done
TransStore html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo3WcQB/R.INSTALLc904cd26352/gQTLstats/man/TransStore.Rd:18: file link 'Registry' in package 'BatchJobs' does not exist and so has been treated as a topic
cisAssoc html
clipPCs html
directPlot html
enumerateByFDR html
eqBox2 html
filtFDR html
gQTLs html
gQTLstats-package html
hmm878 html
manhWngr html
mixedVCFtoSnpMatrix html
pifdr html
qqStore html
queryVCF html
senstab html
setFDRfunc html
storeToStats html
tqbrowser html
transAssoc html
transBrowse html
tsByRank html
txsPlot 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 'gQTLstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLstats' as gQTLstats_1.20.0.zip
* DONE (gQTLstats)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gQTLstats' successfully unpacked and MD5 sums checked
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gQTLstats.Rcheck/tests_i386/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> BiocGenerics:::testPackage("gQTLstats")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: geuvPack
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
clipping PCs 1,2 from exprs
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
Loading required package: geuvStore2
Loading required package: BatchJobs
Loading required package: BBmisc
Attaching package: 'BBmisc'
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:BiocGenerics':
normalize
The following object is masked from 'package:base':
isFALSE
The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files:
1: C:/Users/biocbuild/bbs-3.11-bioc/R/library/BatchJobs/etc/BatchJobs_global_config.R
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
measure.mem: TRUE
Loading required package: gQTLBase
NOTE: there were 41 samples not found (of 462 requested).
using assay() to extract 'expression' matrix from RangedSummarizedExperiment
counting tests...
counting #NA...
obtaining assoc quantiles...
computing perm_assoc histogram....
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
RUNIT TEST PROTOCOL -- Sat Oct 17 05:09:13 2020
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gQTLstats RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(x, ...) : non-diploid variants are set to NA
2: In col.summary(gtdata[[1]]) :
69 rows were empty - ignored when calculating call rates
3: In .local(x, ...) : non-diploid variants are set to NA
4: In col.summary(gtdata$genotypes) :
69 rows were empty - ignored when calculating call rates
5: executing %dopar% sequentially: no parallel backend registered
6: In .local(x, ...) : non-diploid variants are set to NA
7: In .local(x, ...) : non-diploid variants are set to NA
8: In col.summary(gtdata[[1]]) :
238 rows were empty - ignored when calculating call rates
9: In .local(x, ...) : non-diploid variants are set to NA
10: In col.summary(gtdata$genotypes) :
238 rows were empty - ignored when calculating call rates
>
> proc.time()
user system elapsed
299.90 17.35 611.46
|
gQTLstats.Rcheck/tests_x64/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-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.
> BiocGenerics:::testPackage("gQTLstats")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: geuvPack
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
clipping PCs 1,2 from exprs
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
Loading required package: geuvStore2
Loading required package: BatchJobs
Loading required package: BBmisc
Attaching package: 'BBmisc'
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:BiocGenerics':
normalize
The following object is masked from 'package:base':
isFALSE
The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files:
1: C:/Users/biocbuild/bbs-3.11-bioc/R/library/BatchJobs/etc/BatchJobs_global_config.R
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
measure.mem: TRUE
Loading required package: gQTLBase
NOTE: there were 41 samples not found (of 462 requested).
using assay() to extract 'expression' matrix from RangedSummarizedExperiment
counting tests...
counting #NA...
obtaining assoc quantiles...
computing perm_assoc histogram....
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
RUNIT TEST PROTOCOL -- Sat Oct 17 05:14:49 2020
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gQTLstats RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(x, ...) : non-diploid variants are set to NA
2: In col.summary(gtdata[[1]]) :
69 rows were empty - ignored when calculating call rates
3: In .local(x, ...) : non-diploid variants are set to NA
4: In col.summary(gtdata$genotypes) :
69 rows were empty - ignored when calculating call rates
5: executing %dopar% sequentially: no parallel backend registered
6: In .local(x, ...) : non-diploid variants are set to NA
7: In .local(x, ...) : non-diploid variants are set to NA
8: In col.summary(gtdata[[1]]) :
238 rows were empty - ignored when calculating call rates
9: In .local(x, ...) : non-diploid variants are set to NA
10: In col.summary(gtdata$genotypes) :
238 rows were empty - ignored when calculating call rates
>
> proc.time()
user system elapsed
280.18 6.56 335.45
|
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gQTLstats.Rcheck/examples_i386/gQTLstats-Ex.timings
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gQTLstats.Rcheck/examples_x64/gQTLstats-Ex.timings
|