Multiple platform build/check report for BioC 3.7 - CHECK report for transcriptogramer on tokay2

Package: transcriptogramer

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptogramer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings transcriptogramer_1.2.1.tar.gz

StartedAt: 2018-10-17 05:14:34 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 05:19:22 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 287.2 seconds

RetCode: 0

Status: OK

CheckDir: transcriptogramer.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptogramer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings transcriptogramer_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/transcriptogramer.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'transcriptogramer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'transcriptogramer' version '1.2.1'
* 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 'transcriptogramer' 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 ... NOTE
differentiallyExpressed,Transcriptogram: no visible binding for global
  variable 'x'
differentiallyExpressed,Transcriptogram: no visible binding for global
  variable 'y'
differentiallyExpressed,Transcriptogram : <anonymous>: no visible
  binding for global variable 'x'
differentiallyExpressed,Transcriptogram : <anonymous>: no visible
  binding for global variable 'y'
Undefined global functions or variables:
  x y
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/transcriptogramer.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/transcriptogramer_1.2.1.tar.gz && rm -rf transcriptogramer.buildbin-libdir && mkdir transcriptogramer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptogramer.buildbin-libdir transcriptogramer_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL transcriptogramer_1.2.1.zip && rm transcriptogramer_1.2.1.tar.gz transcriptogramer_1.2.1.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 3164k  100 3164k    0     0  35.5M      0 --:--:-- --:--:-- --:--:-- 38.6M

install for i386

* installing *source* package 'transcriptogramer' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'transcriptogramer'
    finding HTML links ... done
    DE-method                               html  
    DEsymbols                               html  
    GPL570                                  html  
    GSE9988                                 html  
    Hs700                                   html  
    Hs800                                   html  
    Hs900                                   html  
    HsBPTerms                               html  
    Mm700                                   html  
    Mm800                                   html  
    Mm900                                   html  
    Rn700                                   html  
    Rn800                                   html  
    Rn900                                   html  
    Sc700                                   html  
    Sc800                                   html  
    Sc900                                   html  
    Transcriptogram-class                   html  
    association                             html  
    clusterEnrichment-method                html  
    clusterVisualization-method             html  
    connectivityProperties-method           html  
    differentiallyExpressed-method          html  
    orderingProperties-method               html  
    radius-method                           html  
    transcriptogramPreprocess               html  
    transcriptogramStep1-method             html  
    transcriptogramStep2-method             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'transcriptogramer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptogramer' as transcriptogramer_1.2.1.zip
* DONE (transcriptogramer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'transcriptogramer' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("transcriptogramer")

preprocessing the input data... step 1 of 1
calculating node properties... step 1 of 2
** this may take some time...
applying sliding window and mounting resulting data... step 2 of 2
** this may take some time...
done!
mapping identifiers to ENSEMBL Peptide ID... step 1 of 2
calculating average over all identifiers related to the same protein... step 2 of 2
done!
applying sliding window and mounting resulting data... step 1 of 1
done!


RUNIT TEST PROTOCOL -- Wed Oct 17 05:18:15 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
transcriptogramer RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   9.62    0.89   56.71


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("transcriptogramer")

preprocessing the input data... step 1 of 1
calculating node properties... step 1 of 2
** this may take some time...
applying sliding window and mounting resulting data... step 2 of 2
** this may take some time...
done!
mapping identifiers to ENSEMBL Peptide ID... step 1 of 2
calculating average over all identifiers related to the same protein... step 2 of 2
done!
applying sliding window and mounting resulting data... step 1 of 1
done!


RUNIT TEST PROTOCOL -- Wed Oct 17 05:19:15 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
transcriptogramer RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  10.64    1.10   59.23

name	user	system	elapsed
DE-method	0.97	0.02	0.98
DEsymbols	0.03	0.00	0.03
GPL570	0.33	0.12	0.46
GSE9988	0.68	0.20	0.90
Hs700	0.05	0.07	0.11
Hs800	0.08	0.01	0.10
Hs900	0.05	0.03	0.07
HsBPTerms	0.84	0.24	1.08
Mm700	0.12	0.03	0.16
Mm800	0.13	0.01	0.14
Mm900	0.06	0.05	0.11
Rn700	0.06	0.11	0.18
Rn800	0.11	0.03	0.14
Rn900	0.09	0.02	0.11
Sc700	0.05	0.00	0.04
Sc800	0.03	0.00	0.03
Sc900	0.01	0.01	0.03
association	0.00	0.02	0.01
clusterEnrichment-method	0.12	0.03	0.16
clusterVisualization-method	0.10	0.00	0.09
connectivityProperties-method	0.06	0.00	0.07
differentiallyExpressed-method	0.08	0.02	0.09
orderingProperties-method	0.09	0.00	0.09
radius-method	0.42	0.03	0.46
transcriptogramPreprocess	0.05	0.00	0.05
transcriptogramStep1-method	0.04	0.01	0.06
transcriptogramStep2-method	0.08	0.02	0.09

name	user	system	elapsed
DE-method	1.12	0.05	1.17
DEsymbols	0.02	0.01	0.03
GPL570	0.35	0.08	0.43
GSE9988	0.59	0.22	0.81
Hs700	0.10	0.05	0.14
Hs800	0.07	0.03	0.11
Hs900	0.08	0.01	0.09
HsBPTerms	1.03	0.25	1.28
Mm700	0.08	0.04	0.12
Mm800	0.05	0.07	0.11
Mm900	0.04	0.04	0.10
Rn700	0.08	0.05	0.13
Rn800	0.06	0.06	0.12
Rn900	0.06	0.03	0.10
Sc700	0.05	0.00	0.04
Sc800	0.02	0.02	0.04
Sc900	0.01	0.02	0.03
association	0.03	0.00	0.03
clusterEnrichment-method	0.10	0.04	0.14
clusterVisualization-method	0.18	0.02	0.20
connectivityProperties-method	0.74	0.03	0.77
differentiallyExpressed-method	0.06	0.03	0.09
orderingProperties-method	0.14	0.00	0.14
radius-method	0.06	0.02	0.08
transcriptogramPreprocess	0.07	0.04	0.11
transcriptogramStep1-method	0.09	0.00	0.09
transcriptogramStep2-method	0.11	0.02	0.13

CHECK report for transcriptogramer on tokay2

Summary

Command output

Installation output

Tests output

Example timings