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This page was generated on 2022-01-19 13:06:54 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for metaSeq on tokay2


To the developers/maintainers of the metaSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaSeq.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.

raw results

Package 1105/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaSeq 1.34.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/metaSeq
git_branch: RELEASE_3_14
git_last_commit: 08a332b
git_last_commit_date: 2021-10-26 12:10:48 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metaSeq
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metaSeq_1.34.0.tar.gz
StartedAt: 2022-01-18 22:18:00 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 22:19:40 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 99.8 seconds
RetCode: 0
Status:   OK  
CheckDir: metaSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metaSeq_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/metaSeq.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.34.0'
* 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-3.14-bioc/meat/metaSeq.Rcheck/00check.log'
for details.



Installation output

metaSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/metaSeq_1.34.0.tar.gz && rm -rf metaSeq.buildbin-libdir && mkdir metaSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaSeq.buildbin-libdir metaSeq_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL metaSeq_1.34.0.zip && rm metaSeq_1.34.0.tar.gz metaSeq_1.34.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 17 6245k   17 1112k    0     0  5016k      0  0:00:01 --:--:--  0:00:01 5012k
100 6245k  100 6245k    0     0  16.6M      0 --:--:-- --:--:-- --:--:-- 16.7M

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_1.34.0.zip
* DONE (metaSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'metaSeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

metaSeq.Rcheck/examples_i386/metaSeq-Ex.timings

nameusersystemelapsed
BreastCancer0.090.020.11
Fisher.test1.350.051.39
Result.Meta0.170.000.17
Stouffer.test1.080.001.08
StudyA0.170.030.20
meta.oneside.noiseq1.150.061.22
meta.readData1.190.001.19
other.oneside.pvalues0.010.000.02
pvals1.320.061.37

metaSeq.Rcheck/examples_x64/metaSeq-Ex.timings

nameusersystemelapsed
BreastCancer0.080.000.08
Fisher.test1.280.021.30
Result.Meta0.140.000.14
Stouffer.test1.070.001.08
StudyA0.150.010.16
meta.oneside.noiseq1.540.001.54
meta.readData1.240.021.25
other.oneside.pvalues0.030.000.04
pvals1.370.031.40