Alex Pickering
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/crossmeta |
| Branch: RELEASE_3_12 |
| Last Commit: 02d63d6 |
| Last Changed Date: 2020-11-02 13:21:38 -0400 (Mon, 02 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:31 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the crossmeta package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 400/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crossmeta 1.16.1 (landing page) Alex Pickering
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: crossmeta |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings crossmeta_1.16.1.tar.gz |
| StartedAt: 2021-05-06 01:52:38 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:55:40 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 182.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: crossmeta.Rcheck |
| Warnings: 4 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings crossmeta_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.16.1'
* 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 'crossmeta' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpoNQjf0/R.INSTALL24302e3f849/crossmeta/man/es_meta.Rd:38: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpoNQjf0/R.INSTALL24302e3f849/crossmeta/man/exprs.MA.Rd:17: file link 'plotDensities.MAList' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpoNQjf0/R.INSTALL24302e3f849/crossmeta/man/exprs.MA.Rd:17: file link 'exprs.MA' in package 'limma' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-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 ... WARNING
'::' or ':::' import not declared from: 'tibble'
Namespace in Imports field not imported from: 'statmod'
All declared Imports should be used.
Unexported object imported by a ':::' call: 'GEOquery:::parseGSEMatrix'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'getDirListing' 'getGEO' 'getGEOSuppFiles'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_contrasts: no visible global function definition for
'select_contrasts'
bulkAnnot : <anonymous>: no visible global function definition for
'write.csv'
bulkAnnot: no visible global function definition for 'html'
bulkAnnot: no visible global function definition for 'toggleClass'
bulkAnnot: no visible global function definition for 'read.csv'
diff_anal: no visible global function definition for 'model.matrix'
getAndParseGSEMatrices: no visible global function definition for
'download.file'
getDirListing: no visible global function definition for 'read.table'
getGEOSuppFiles: no visible global function definition for
'download.file'
get_palette: no visible global function definition for 'head'
is_invertible: no visible global function definition for 'is'
load_agil_plat : <anonymous>: no visible global function definition for
'capture.output'
load_raw: no visible global function definition for 'setNames'
symbol_annot: no visible binding for global variable 'SYMBOL_9606'
to_eset: no visible global function definition for 'as'
to_ma: no visible global function definition for 'new'
which_max_iqr: no visible binding for global variable 'iqrange'
xls_to_txt: no visible global function definition for 'write.table'
Undefined global functions or variables:
SYMBOL_9606 as capture.output download.file head html iqrange is
model.matrix new read.csv read.table select_contrasts setNames
toggleClass write.csv write.table
Consider adding
importFrom("methods", "as", "is", "new")
importFrom("stats", "model.matrix", "setNames")
importFrom("utils", "capture.output", "download.file", "head",
"read.csv", "read.table", "write.csv", "write.table")
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 ... WARNING
Codoc mismatches from documentation object 'add_sources':
add_sources
Code: function(diff_exprs, data_dir = getwd(), postfix = NULL)
Docs: function(diff_exprs, data_dir = getwd())
Argument names in code not in docs:
postfix
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ch2_subset'
'prev_anal'
Undocumented arguments in documentation object 'get_sva_mods'
'pdata'
Documented arguments not in \usage in documentation object 'get_sva_mods':
'eset'
Undocumented arguments in documentation object 'iqr_replicates'
'eset'
Documented arguments not in \usage in documentation object 'iqr_replicates':
'mod' 'svobj'
Undocumented arguments in documentation object 'run_select_contrasts'
'port'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 R/sysdata.rda ... 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
symbol_annot 5.81 0.17 5.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
symbol_annot 6 0.23 6.19
* 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 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck/00check.log'
for details.
crossmeta.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/crossmeta_1.16.1.tar.gz && rm -rf crossmeta.buildbin-libdir && mkdir crossmeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crossmeta.buildbin-libdir crossmeta_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL crossmeta_1.16.1.zip && rm crossmeta_1.16.1.tar.gz crossmeta_1.16.1.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
100 3866k 100 3866k 0 0 12.7M 0 --:--:-- --:--:-- --:--:-- 12.8M
install for i386
* installing *source* package 'crossmeta' ...
** 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 'crossmeta'
finding HTML links ... done
addContrastInput html
add_adjusted html
add_sources html
bulkAnnot html
bulkAnnotInput html
bulkForm html
bulkFormInput html
bulkPage html
bulkPageUI html
bulkTable html
bulkTableOuput html
ch2_subset html
delContrastsInput html
diff_expr html
es_meta html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpoNQjf0/R.INSTALL24302e3f849/crossmeta/man/es_meta.Rd:38: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
exprs.MA html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpoNQjf0/R.INSTALL24302e3f849/crossmeta/man/exprs.MA.Rd:17: file link 'plotDensities.MAList' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpoNQjf0/R.INSTALL24302e3f849/crossmeta/man/exprs.MA.Rd:17: file link 'exprs.MA' in package 'limma' does not exist and so has been treated as a topic
fix_illum_headers html
finding level-2 HTML links ... done
format_dl_annot html
format_up_annot html
get_ch2_mod html
get_group_levels html
get_palette html
get_raw html
get_sva_mods html
gs.names html
gslist html
ilmn.nnum html
iqr_replicates html
is_invertible html
load_agil_plat html
load_diff html
load_raw html
open_raw_illum html
phenoData.ch2 html
prefix_illum_headers html
query_ref html
run_select_contrasts html
run_sva html
setup_prev html
symbol_annot html
to_eset html
to_ma html
validate_up_annot html
which_max_iqr html
xls_to_txt 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_1.16.1.zip
* DONE (crossmeta)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'crossmeta' successfully unpacked and MD5 sums checked
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crossmeta.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(crossmeta)
>
> test_check("crossmeta")
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by column names.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Apoa1_ApoAI...-C57BL.6 (# p < 0.05): 20
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
33.25 0.89 34.28
|
crossmeta.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(crossmeta)
>
> test_check("crossmeta")
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by column names.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Apoa1_ApoAI...-C57BL.6 (# p < 0.05): 20
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
39.43 0.34 40.15
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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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