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CHECK report for PepsNMR on tokay1

This page was generated on 2019-04-13 11:29:56 -0400 (Sat, 13 Apr 2019).

Package 1141/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PepsNMR 1.0.2
Manon Martin
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/PepsNMR
Branch: RELEASE_3_8
Last Commit: aebf0b2
Last Changed Date: 2019-03-08 06:09:00 -0400 (Fri, 08 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] 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: PepsNMR
Version: 1.0.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PepsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PepsNMR_1.0.2.tar.gz
StartedAt: 2019-04-13 04:27:33 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:35:44 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 491.6 seconds
RetCode: 0
Status:  OK  
CheckDir: PepsNMR.Rcheck
Warnings: 0

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:PepsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PepsNMR_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PepsNMR.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 'PepsNMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PepsNMR' version '1.0.2'
* package encoding: UTF-8
* 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 'PepsNMR' can be installed ... OK
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
PEPSNMR-package    102.12   7.76  110.35
PreprocessingChain  85.66   4.89   90.54
Warping             10.83   0.56   11.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
PEPSNMR-package    57.92   6.20   64.17
PreprocessingChain 50.80   5.06   55.86
Warping             8.31   0.78    9.09
* 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: OK


Installation output

PepsNMR.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/PepsNMR_1.0.2.tar.gz && rm -rf PepsNMR.buildbin-libdir && mkdir PepsNMR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PepsNMR.buildbin-libdir PepsNMR_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PepsNMR_1.0.2.zip && rm PepsNMR_1.0.2.tar.gz PepsNMR_1.0.2.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  150k  100  150k    0     0  3632k      0 --:--:-- --:--:-- --:--:-- 3971k

install for i386

* installing *source* package 'PepsNMR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PepsNMR'
    finding HTML links ... done
    Apodization                             html  
    BaselineCorrection                      html  
    Bucketing                               html  
    Draw                                    html  
    DrawPCA                                 html  
    DrawSignal                              html  
    FirstOrderPhaseCorrection               html  
    FourierTransform                        html  
    GroupDelayCorrection                    html  
    InternalReferencing                     html  
    NegativeValuesZeroing                   html  
    Normalization                           html  
    PEPSNMR-internal                        html  
    PEPSNMR-package                         html  
    PreprocessingChain                      html  
    ReadFids                                html  
    RegionRemoval                           html  
    SolventSuppression                      html  
    Warping                                 html  
    WindowSelection                         html  
    ZeroOrderPhaseCorrection                html  
    ZoneAggregation                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PepsNMR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PepsNMR' as PepsNMR_1.0.2.zip
* DONE (PepsNMR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PepsNMR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

PepsNMR.Rcheck/examples_i386/PepsNMR-Ex.timings

nameusersystemelapsed
Apodization0.810.091.28
BaselineCorrection0.700.160.86
Bucketing0.110.000.11
Draw1.890.062.03
DrawPCA1.310.051.41
DrawSignal1.030.031.06
FirstOrderPhaseCorrection0.050.020.06
FourierTransform0.060.000.07
GroupDelayCorrection0.060.010.07
InternalReferencing0.060.020.08
NegativeValuesZeroing0.020.000.02
Normalization0.020.000.01
PEPSNMR-package102.12 7.76110.35
PreprocessingChain85.66 4.8990.54
ReadFids0.360.070.43
RegionRemoval0.010.000.01
SolventSuppression0.130.000.13
Warping10.83 0.5611.40
WindowSelection0.030.000.03
ZeroOrderPhaseCorrection0.090.000.10
ZoneAggregation0.310.020.86

PepsNMR.Rcheck/examples_x64/PepsNMR-Ex.timings

nameusersystemelapsed
Apodization0.610.030.64
BaselineCorrection0.490.160.64
Bucketing0.060.010.08
Draw1.510.001.52
DrawPCA0.720.050.76
DrawSignal0.720.030.75
FirstOrderPhaseCorrection0.030.000.04
FourierTransform0.030.000.03
GroupDelayCorrection0.070.020.07
InternalReferencing0.030.000.04
NegativeValuesZeroing0.010.000.01
Normalization0.020.000.02
PEPSNMR-package57.92 6.2064.17
PreprocessingChain50.80 5.0655.86
ReadFids0.330.020.34
RegionRemoval000
SolventSuppression0.120.000.13
Warping8.310.789.09
WindowSelection0.040.000.03
ZeroOrderPhaseCorrection0.060.000.06
ZoneAggregation0.360.000.36