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CHECK report for SimBindProfiles on tokay1

This page was generated on 2019-04-13 11:23:15 -0400 (Sat, 13 Apr 2019).

Package 1450/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SimBindProfiles 1.20.0
Bettina Fischer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SimBindProfiles
Branch: RELEASE_3_8
Last Commit: 2fad013
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SimBindProfiles
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SimBindProfiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SimBindProfiles_1.20.0.tar.gz
StartedAt: 2019-04-13 05:34:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:38:03 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 242.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SimBindProfiles.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SimBindProfiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SimBindProfiles_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SimBindProfiles.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SimBindProfiles/DESCRIPTION' ... OK
* this is package 'SimBindProfiles' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'SimBindProfiles' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWcT4VX/R.INSTALL1870560d49f8/SimBindProfiles/man/probeAnnoFromESet.Rd:33: file link 'probeAnno-class' in package 'Ringo' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWcT4VX/R.INSTALL1870560d49f8/SimBindProfiles/man/readSgrFiles.Rd:29: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SimBindProfiles.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compensationRegions: no visible global function definition for
  'write.table'
eSetScatterPlot : upPan: no visible global function definition for
  'par'
eSetScatterPlot : upPan: no visible global function definition for
  'smoothScatter'
eSetScatterPlot : lowPan: no visible global function definition for
  'text'
eSetScatterPlot : lowPan: no visible global function definition for
  'par'
eSetScatterPlot : lowPan: no visible global function definition for
  'cor'
eSetScatterPlot: no visible global function definition for 'pairs'
filterRegionsPairwise: no visible global function definition for 'tail'
filterRegionsThreeway: no visible global function definition for 'tail'
findBoundCutoff: no visible global function definition for 'hist'
findBoundCutoff: no visible global function definition for 'p.adjust'
increasedBindingRegions: no visible global function definition for
  'write.table'
normalNull: no visible global function definition for 'na.omit'
normalNull: no visible global function definition for 'density'
normalNull: no visible global function definition for 'sd'
normalNull: no visible global function definition for 'pnorm'
pairwiseRegions: no visible global function definition for
  'write.table'
plotBoundProbes: no visible global function definition for 'points'
probeLengthPlot: no visible global function definition for 'tail'
readSgrFiles: no visible global function definition for 'read.delim'
threewayRegions: no visible global function definition for
  'write.table'
twoGaussiansNull.BF: no visible global function definition for
  'na.omit'
twoGaussiansNull.BF: no visible global function definition for 'dnorm'
twoGaussiansNull.BF: no visible global function definition for 'lines'
twoGaussiansNull.BF: no visible global function definition for 'legend'
twoGaussiansNull.BF: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cor density dnorm hist legend lines na.omit p.adjust pairs par pnorm
  points read.delim sd smoothScatter tail text write.table
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "pairs", "par",
             "points", "smoothScatter", "text")
  importFrom("stats", "cor", "density", "dnorm", "na.omit", "p.adjust",
             "pnorm", "sd")
  importFrom("utils", "read.delim", "tail", "write.table")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/SimBindProfiles.Rcheck/00check.log'
for details.



Installation output

SimBindProfiles.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SimBindProfiles_1.20.0.tar.gz && rm -rf SimBindProfiles.buildbin-libdir && mkdir SimBindProfiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SimBindProfiles.buildbin-libdir SimBindProfiles_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SimBindProfiles_1.20.0.zip && rm SimBindProfiles_1.20.0.tar.gz SimBindProfiles_1.20.0.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 1499k  100 1499k    0     0  18.1M      0 --:--:-- --:--:-- --:--:-- 19.0M

install for i386

* installing *source* package 'SimBindProfiles' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SimBindProfiles'
    finding HTML links ... done
    SGR                                     html  
    SimBindProfiles-package                 html  
    compensationRegions                     html  
    eSetScatterPlot                         html  
    findBoundCutoff                         html  
    increasedBindingRegions                 html  
    pairwiseRegions                         html  
    plotBoundProbes                         html  
    probeAnnoFromESet                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWcT4VX/R.INSTALL1870560d49f8/SimBindProfiles/man/probeAnnoFromESet.Rd:33: file link 'probeAnno-class' in package 'Ringo' does not exist and so has been treated as a topic
    probeLengthPlot                         html  
    readSgrFiles                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWcT4VX/R.INSTALL1870560d49f8/SimBindProfiles/man/readSgrFiles.Rd:29: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    threewayRegions                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SimBindProfiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SimBindProfiles' as SimBindProfiles_1.20.0.zip
* DONE (SimBindProfiles)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SimBindProfiles' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SimBindProfiles.Rcheck/examples_i386/SimBindProfiles-Ex.timings

nameusersystemelapsed
SGR0.400.040.51
compensationRegions1.210.001.21
eSetScatterPlot1.300.241.53
findBoundCutoff3.640.113.75
increasedBindingRegions1.160.011.18
pairwiseRegions1.260.071.32
plotBoundProbes1.810.011.83
probeAnnoFromESet0.890.050.94
probeLengthPlot1.600.011.61
readSgrFiles0.120.000.28
threewayRegions1.610.081.69

SimBindProfiles.Rcheck/examples_x64/SimBindProfiles-Ex.timings

nameusersystemelapsed
SGR0.560.020.57
compensationRegions1.540.031.57
eSetScatterPlot1.280.141.42
findBoundCutoff3.940.084.02
increasedBindingRegions0.720.060.78
pairwiseRegions1.690.101.78
plotBoundProbes1.360.031.39
probeAnnoFromESet1.200.011.22
probeLengthPlot1.750.021.76
readSgrFiles0.210.000.21
threewayRegions1.900.112.01