VJ Carey
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/gwascat |
| Branch: RELEASE_3_11 |
| Last Commit: 97258a1 |
| Last Changed Date: 2020-05-02 10:36:06 -0400 (Sat, 02 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:48 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE gwascat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 796/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gwascat 2.20.1 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.4 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: 2.20.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwascat.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gwascat_2.20.1.tar.gz |
| StartedAt: 2020-10-17 04:49:58 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:04:41 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 882.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gwascat.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwascat.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gwascat_2.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gwascat.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 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.20.1'
* 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 53.1Mb
sub-directories of 1Mb or more:
data 45.0Mb
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: 'BiocGenerics'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'snpsBySeqname'
chklocs: no visible global function definition for 'start'
gwdf2GRanges: no visible global function definition for 'new'
lo38to19: no visible global function definition for 'liftOver'
lo38to19: no visible global function definition for 'sessionInfo'
lo38to19: no visible binding for global variable 'si.hs.37'
lo38to19: no visible global function definition for 'new'
locs4trait: no visible global function definition for 'new'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat: no visible global function definition for
'sessionInfo'
makeCurrentGwascat.legacy: no visible binding for global variable
'si.hs.38'
obo2graphNEL: no visible global function definition for 'new'
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'
[,gwaswloc-ANY-ANY-ANY: no visible global function definition for 'new'
show,gwaswloc: no visible global function definition for 'show'
Undefined global functions or variables:
PVALUE_MLOG getSNPlocs gwrngs gwrngs19 liftOver new phr sessionInfo
show si.hs.37 si.hs.38 snpsBySeqname start
Consider adding
importFrom("methods", "new", "show")
importFrom("stats", "start")
importFrom("utils", "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 6 marked Latin-1 strings
Note: found 53 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
gwcex2gviz 8.76 1.24 12.76
ldtagr 3.72 1.01 6.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gwcex2gviz 9.46 0.33 9.81
riskyAlleleCount 5.07 0.14 5.22
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/gwascat.Rcheck/00check.log'
for details.
gwascat.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/gwascat_2.20.1.tar.gz && rm -rf gwascat.buildbin-libdir && mkdir gwascat.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gwascat.buildbin-libdir gwascat_2.20.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gwascat_2.20.1.zip && rm gwascat_2.20.1.tar.gz gwascat_2.20.1.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
2 43.9M 2 912k 0 0 2689k 0 0:00:16 --:--:-- 0:00:16 2738k
100 43.9M 100 43.9M 0 0 38.0M 0 0:00:01 0:00:01 --:--:-- 38.2M
install for i386
* installing *source* package 'gwascat' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
ebicat37 html
ebicat37UCSC html
ebicat_b37 html
ebicat_b38 html
gwascat-package html
gwastagger html
gwaswloc-class html
gwcex2gviz html
gwdf_2012_02_02 html
ldtagr html
locon6 html
locs4trait html
makeCurrentGwascat html
obo2graphNEL html
riskyAlleleCount html
si.hs.37 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_2.20.1.zip
* DONE (gwascat)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gwascat' successfully unpacked and MD5 sums checked
|
gwascat.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("gwascat")
gwascat loaded. Use makeCurrentGwascat() to extract current image.
from EBI. The data folder of this package has some legacy extracts.
RUNIT TEST PROTOCOL -- Sat Oct 17 05:03:56 2020
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gwascat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.70 0.95 15.92
|
gwascat.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("gwascat")
gwascat loaded. Use makeCurrentGwascat() to extract current image.
from EBI. The data folder of this package has some legacy extracts.
RUNIT TEST PROTOCOL -- Sat Oct 17 05:04:12 2020
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gwascat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.09 0.51 16.31
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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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