Koki Tsuyuzaki
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/metaSeq |
| Branch: RELEASE_3_11 |
| Last Commit: 7ff1efb |
| Last Changed Date: 2020-04-27 14:37:21 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:03 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE metaSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1042/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metaSeq 1.28.0 Koki Tsuyuzaki
| 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: metaSeq |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metaSeq_1.28.0.tar.gz |
| StartedAt: 2020-10-17 05:50:41 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:52:32 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 111.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metaSeq_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metaSeq.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 'metaSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaSeq' version '1.28.0'
* 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 'metaSeq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Unexported objects imported by ':::' calls:
'NOISeq:::busca' 'NOISeq:::n.menor'
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:
'oneside.noiseq'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'metaSeq/R/Accelerate.NOISeq.R':
assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
File 'metaSeq/R/Reset.Accelerate.NOISeq.R':
assignInNamespace("busca", original.busca, ns = "NOISeq", envir = env)
assignInNamespace("n.menor", original.n.menor, ns = "NOISeq",
envir = env)
File 'metaSeq/R/oneside.noiseq.R':
assignInNamespace("probdeg", custom.probdeg, ns = "NOISeq", envir = env)
assignInNamespace("MD", custom.MD, ns = "NOISeq", envir = env)
assignInNamespace("probdeg", original.probdeg, ns = "NOISeq",
envir = env)
assignInNamespace("MD", original.MD, ns = "NOISeq", envir = env)
Accelerate.NOISeq: no visible global function definition for 'data'
Accelerate.NOISeq: no visible binding for global variable
'text.n.menor_unix'
Accelerate.NOISeq: no visible binding for global variable
'text.busca_unix'
Accelerate.NOISeq: no visible global function definition for
'assignInNamespace'
Accelerate.NOISeq: no visible binding for global variable 'busca'
Accelerate.NOISeq: no visible binding for global variable 'nmenor'
Accelerate.NOISeq: no visible binding for global variable
'text.n.menor_win'
Accelerate.NOISeq: no visible binding for global variable
'text.busca_win'
Reset.Accelerate.NOISeq: no visible global function definition for
'assignInNamespace'
custom.MD: no visible global function definition for 'combn'
custom.probdeg: no visible global function definition for 'na.omit'
each.Fisher.ignore.test: no visible global function definition for
'pchisq'
each.Fisher.test: no visible global function definition for 'pchisq'
each.Stouffer.ignore.test: no visible global function definition for
'qnorm'
each.Stouffer.ignore.test: no visible global function definition for
'pnorm'
each.Stouffer.test: no visible global function definition for 'qnorm'
each.Stouffer.test: no visible global function definition for 'pnorm'
oneside.noiseq: no visible global function definition for
'assignInNamespace'
original.MD: no visible global function definition for 'combn'
original.probdeg: no visible global function definition for 'na.omit'
original.probdeg: no visible binding for global variable 'n.menor'
original.probdeg: no visible binding for global variable 'busca'
Undefined global functions or variables:
assignInNamespace busca combn data n.menor na.omit nmenor pchisq
pnorm qnorm text.busca_unix text.busca_win text.n.menor_unix
text.n.menor_win
Consider adding
importFrom("stats", "na.omit", "pchisq", "pnorm", "qnorm")
importFrom("utils", "assignInNamespace", "combn", "data")
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'Fig1.jpeg', 'Fig2.png'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/metaSeq.Rcheck/00check.log'
for details.
metaSeq.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/metaSeq_1.28.0.tar.gz && rm -rf metaSeq.buildbin-libdir && mkdir metaSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaSeq.buildbin-libdir metaSeq_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL metaSeq_1.28.0.zip && rm metaSeq_1.28.0.tar.gz metaSeq_1.28.0.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 6243k 100 6243k 0 0 22.6M 0 --:--:-- --:--:-- --:--:-- 23.2M
install for i386
* installing *source* package 'metaSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metaSeq'
finding HTML links ... done
Accelerate.NOISeq html
BreastCancer html
Fisher.test html
Reset.Accelerate.NOISeq html
Result.Meta html
Stouffer.test html
StudyA html
meta.oneside.noiseq html
meta.readData html
metaSeq-package html
other.oneside.pvalues html
pvals html
text.busca_unix html
text.busca_win html
text.n.menor_unix html
text.n.menor_win 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 'metaSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaSeq' as metaSeq_1.28.0.zip
* DONE (metaSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'metaSeq' successfully unpacked and MD5 sums checked
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metaSeq.Rcheck/examples_i386/metaSeq-Ex.timings
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metaSeq.Rcheck/examples_x64/metaSeq-Ex.timings
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