VJ Carey
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/gwascat |
| git_branch: RELEASE_3_13 |
| git_last_commit: d251baa |
| git_last_commit_date: 2021-05-19 11:51:31 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the gwascat package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gwascat.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 833/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gwascat 2.24.0 (landing page) VJ Carey
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: gwascat |
| Version: 2.24.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwascat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings gwascat_2.24.0.tar.gz |
| StartedAt: 2021-10-15 00:12:51 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:25:36 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 765.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gwascat.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwascat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings gwascat_2.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/gwascat.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.24.0'
* package encoding: UTF-8
* 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 34.2Mb
sub-directories of 1Mb or more:
data 10.1Mb
legacy 15.6Mb
obo 3.0Mb
olddata 2.2Mb
tab 1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'IRanges'
A package should be listed in only one of these fields.
* 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
addSeqlengths: no visible global function definition for 'seqlengths'
addSeqlengths: no visible global function definition for 'seqlengths<-'
bindcadd_snv: no visible global function definition for 'TabixFile'
bindcadd_snv: no visible global function definition for 'findOverlaps'
buildq: no visible global function definition for 'read.delim'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'snpsBySeqname'
gwascat_from_AHub: no visible global function definition for 'data'
gwascat_from_AHub: no visible binding for global variable 'si.hs.38'
gwascat_from_AHub: no visible global function definition for
'sessionInfo'
gwcat_snapshot: no visible global function definition for 'data'
gwcat_snapshot: no visible binding for global variable 'si.hs.38'
gwcat_snapshot: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'liftOver'
lo38to19: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'data'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible global function definition for
'download.file'
makeCurrentGwascat: no visible global function definition for 'data'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat: no visible global function definition for
'sessionInfo'
process_gwas_dataframe: no visible global function definition for
'data'
process_gwas_dataframe: no visible binding for global variable
'si.hs.38'
process_gwas_dataframe: no visible global function definition for
'sessionInfo'
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 global function definition for 'aes'
traitsManh: no visible binding for global variable 'PVALUE_MLOG'
variantProps: no visible binding for global variable 'gwrngs'
Undefined global functions or variables:
PVALUE_MLOG TabixFile aes data download.file findOverlaps getSNPlocs
gwrngs gwrngs19 liftOver phr read.delim seqlengths seqlengths<-
sessionInfo si.hs.37 si.hs.38 snpsBySeqname
Consider adding
importFrom("utils", "data", "download.file", "read.delim",
"sessionInfo")
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 ... NOTE
Note: found 2 marked Latin-1 strings
Note: found 2075 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
gwascat_from_AHub 54.01 1.45 56.60
gwcat_snapshot 48.36 1.35 50.45
gwcex2gviz 9.36 0.25 9.61
gg17N 8.11 0.06 8.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gwascat_from_AHub 46.45 1.10 48.58
gwcat_snapshot 44.36 0.79 45.86
gwcex2gviz 10.16 0.33 10.48
gg17N 7.98 0.06 8.05
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/gwascat.Rcheck/00check.log'
for details.
gwascat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/gwascat_2.24.0.tar.gz && rm -rf gwascat.buildbin-libdir && mkdir gwascat.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gwascat.buildbin-libdir gwascat_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL gwascat_2.24.0.zip && rm gwascat_2.24.0.tar.gz gwascat_2.24.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
5 32.8M 5 1861k 0 0 1821k 0 0:00:18 0:00:01 0:00:17 1821k
14 32.8M 14 4769k 0 0 2365k 0 0:00:14 0:00:02 0:00:12 2364k
24 32.8M 24 8391k 0 0 2772k 0 0:00:12 0:00:03 0:00:09 2772k
38 32.8M 38 12.6M 0 0 3207k 0 0:00:10 0:00:04 0:00:06 3207k
55 32.8M 55 18.0M 0 0 3677k 0 0:00:09 0:00:05 0:00:04 3704k
72 32.8M 72 23.8M 0 0 4052k 0 0:00:08 0:00:06 0:00:02 4508k
91 32.8M 91 29.9M 0 0 4370k 0 0:00:07 0:00:07 --:--:-- 5179k
100 32.8M 100 32.8M 0 0 4507k 0 0:00:07 0:00:07 --:--:-- 5694k
install for i386
* installing *source* package 'gwascat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gwascat'
finding HTML links ... done
bindcadd_snv html
chklocs html
ebicat_2020_04_30 html
g17SM html
getRsids-gwaswloc-method html
getRsids html
getTraits-gwaswloc-method html
getTraits html
get_cached_gwascat html
gg17N html
gr6.0_hg38 html
gw6.rs_17 html
gwascat_from_AHub html
gwastagger html
gwaswloc-class html
gwcat_snapshot html
gwcex2gviz html
ldtagr html
locon6 html
locs4trait html
low17 html
makeCurrentGwascat html
obo2graphNEL html
process_gwas_dataframe html
riskyAlleleCount html
si.hs.37 html
si.hs.38 html
sub-gwaswloc-ANY-ANY-ANY-method html
subsetByChromosome-gwaswloc-method html
subsetByChromosome html
subsetByTraits-gwaswloc-method html
subsetByTraits html
topTraits html
traitsManh 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 'gwascat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gwascat' as gwascat_2.24.0.zip
* DONE (gwascat)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'gwascat' successfully unpacked and MD5 sums checked
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gwascat.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> library(testthat)
>
> test_check("gwascat")
Loading required package: gwascat
gwascat loaded. Use makeCurrentGwascat() to extract current image.
from EBI. The data folder of this package has some legacy extracts.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
>
> proc.time()
user system elapsed
11.34 0.87 12.20
|
gwascat.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> library(testthat)
>
> test_check("gwascat")
Loading required package: gwascat
gwascat loaded. Use makeCurrentGwascat() to extract current image.
from EBI. The data folder of this package has some legacy extracts.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
>
> proc.time()
user system elapsed
13.54 0.56 14.09
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gwascat.Rcheck/examples_i386/gwascat-Ex.timings
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gwascat.Rcheck/examples_x64/gwascat-Ex.timings
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