Alex Pickering
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/crossmeta |
| Branch: master |
| Last Commit: d0e4576 |
| Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:26:47 -0400 (Tue, 09 Apr 2019).
| Package 361/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| crossmeta 1.9.0 Alex Pickering
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: crossmeta |
| Version: 1.9.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings crossmeta_1.9.0.tar.gz |
| StartedAt: 2019-04-09 02:04:50 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:07:30 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 160.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: crossmeta.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings crossmeta_1.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/crossmeta.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crossmeta/DESCRIPTION' ... OK
* this is package 'crossmeta' version '1.9.0'
* 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 'crossmeta' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqaO1vU/R.INSTALL25d847c338cb/crossmeta/man/es_meta.Rd:37: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/crossmeta.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
Missing or unexported objects:
'crossmeta::gs.names' 'crossmeta::gslist'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
explore_paths : server: no visible binding for global variable 'gslist'
explore_paths : server: no visible binding for global variable
'gs.names'
Undefined global functions or variables:
gs.names gslist
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data with usage in documentation object 'gs.names' but not in code:
gs.names
Data with usage in documentation object 'gslist' but not in code:
gslist
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
diff_path 6.44 0.3 6.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
diff_path 8.08 0.14 8.56
symbol_annot 5.77 0.10 5.96
es_meta 4.81 0.08 5.17
* 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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/crossmeta.Rcheck/00check.log'
for details.
crossmeta.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/crossmeta_1.9.0.tar.gz && rm -rf crossmeta.buildbin-libdir && mkdir crossmeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crossmeta.buildbin-libdir crossmeta_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL crossmeta_1.9.0.zip && rm crossmeta_1.9.0.tar.gz crossmeta_1.9.0.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
100 657k 100 657k 0 0 9894k 0 --:--:-- --:--:-- --:--:-- 10.8M
install for i386
* installing *source* package 'crossmeta' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'crossmeta'
finding HTML links ... done
add_sources html
contribute html
diff_expr html
diff_path html
es_meta html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqaO1vU/R.INSTALL25d847c338cb/crossmeta/man/es_meta.Rd:37: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
explore_paths html
get_raw html
gs.names html
gslist html
load_diff html
load_path html
load_raw html
open_raw_illum html
path_meta html
setup_prev html
symbol_annot 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 'crossmeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crossmeta' as crossmeta_1.9.0.zip
* DONE (crossmeta)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'crossmeta' successfully unpacked and MD5 sums checked
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crossmeta.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> library(crossmeta)
>
> test_check("crossmeta")
AnnotatingAnnotatingAnnotatingGSE1_FOO-VEH (# p < 0.05): 3
GSE1_FOO-VEH (# p < 0.05): 3
GSE1_FOO-VEH (# p < 0.05): 3
== testthat results ===========================================================
OK: 14 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
10.62 0.70 15.06
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crossmeta.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> library(crossmeta)
>
> test_check("crossmeta")
AnnotatingAnnotatingAnnotatingGSE1_FOO-VEH (# p < 0.05): 3
GSE1_FOO-VEH (# p < 0.05): 3
GSE1_FOO-VEH (# p < 0.05): 3
== testthat results ===========================================================
OK: 14 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.60 0.48 13.76
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crossmeta.Rcheck/examples_i386/crossmeta-Ex.timings
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crossmeta.Rcheck/examples_x64/crossmeta-Ex.timings
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