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CHECK report for edge on tokay2

This page was generated on 2018-10-17 08:40:35 -0400 (Wed, 17 Oct 2018).

Package 433/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edge 2.12.2
John D. Storey , Andrew J. Bass
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/edge
Branch: RELEASE_3_7
Last Commit: dfdcbff
Last Changed Date: 2018-08-30 08:49:43 -0400 (Thu, 30 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: edge
Version: 2.12.2
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:edge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings edge_2.12.2.tar.gz
StartedAt: 2018-10-17 01:45:24 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:50:09 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 284.9 seconds
RetCode: 0
Status:  OK  
CheckDir: edge.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:edge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings edge_2.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/edge.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 'edge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'edge' version '2.12.2'
* 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 'edge' 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
build_study: no visible global function definition for 'as.formula'
createSet: no visible global function definition for 'model.matrix'
deSetCheck: no visible global function definition for 'model.matrix'
fitFDist: no visible global function definition for 'median'
fitFDist: no visible global function definition for 'lm.fit'
fitFDist: no visible global function definition for 'predict'
fit_wmodels: no visible global function definition for 'model.matrix'
fit_wmodels: no visible global function definition for 'lm.wfit'
null: no visible global function definition for 'model.matrix'
apply_sva,deSet: no visible global function definition for 'as.formula'
apply_sva,deSet: no visible global function definition for 'terms'
fit_models,deSet: no visible global function definition for
  'model.matrix'
fullModel<-,deSet: no visible global function definition for
  'model.matrix'
lrt,deSet-deFit: no visible global function definition for 'pf'
nullModel<-,deSet: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  as.formula lm.fit lm.wfit median model.matrix pf predict terms
Consider adding
  importFrom("stats", "as.formula", "lm.fit", "lm.wfit", "median",
             "model.matrix", "pf", "predict", "terms")
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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/edge/libs/i386/edge.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
apply_snm 16.1   0.56   16.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
apply_snm 12.84   0.89   13.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/edge.Rcheck/00check.log'
for details.



Installation output

edge.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/edge_2.12.2.tar.gz && rm -rf edge.buildbin-libdir && mkdir edge.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=edge.buildbin-libdir edge_2.12.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL edge_2.12.2.zip && rm edge_2.12.2.tar.gz edge_2.12.2.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
100  658k  100  658k    0     0   9.8M      0 --:--:-- --:--:-- --:--:-- 10.9M

install for i386

* installing *source* package 'edge' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c edge-init.c -o edge-init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c edgeKLODP.c -o edgeKLODP.o
edgeKLODP.c: In function 'odpScoreCluster':
edgeKLODP.c:11:19: warning: 'middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double *first, *middle;
                   ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o edge.dll tmp.def edge-init.o edgeKLODP.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/edge.buildbin-libdir/edge/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'edge'
    finding HTML links ... done
    apply_jackstraw                         html  
    finding level-2 HTML links ... done

    apply_qvalue                            html  
    apply_snm                               html  
    apply_sva                               html  
    betaCoef                                html  
    build_models                            html  
    build_study                             html  
    deFit-class                             html  
    deSet-class                             html  
    deSet                                   html  
    edge                                    html  
    endotoxin                               html  
    fitFull                                 html  
    fitNull                                 html  
    fit_models                              html  
    fullMatrix                              html  
    fullModel                               html  
    gibson                                  html  
    individual                              html  
    kidney                                  html  
    kl_clust                                html  
    lrt                                     html  
    nullMatrix                              html  
    nullModel                               html  
    odp                                     html  
    qvalueObj                               html  
    resFull                                 html  
    resNull                                 html  
    sType                                   html  
    show                                    html  
    summary                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'edge' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c edge-init.c -o edge-init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c edgeKLODP.c -o edgeKLODP.o
edgeKLODP.c: In function 'odpScoreCluster':
edgeKLODP.c:11:19: warning: 'middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double *first, *middle;
                   ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o edge.dll tmp.def edge-init.o edgeKLODP.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/edge.buildbin-libdir/edge/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'edge' as edge_2.12.2.zip
* DONE (edge)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'edge' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

edge.Rcheck/tests_i386/testthat.Rout


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.

> library(testthat)
> library(edge)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("edge")
== testthat results  ===========================================================
OK: 29 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.35    0.62   10.96 

edge.Rcheck/tests_x64/testthat.Rout


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.

> library(testthat)
> library(edge)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("edge")
== testthat results  ===========================================================
OK: 29 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.23    0.45   10.75 

Example timings

edge.Rcheck/examples_i386/edge-Ex.timings

nameusersystemelapsed
apply_jackstraw2.340.052.39
apply_qvalue0.590.090.68
apply_snm16.10 0.5616.66
apply_sva2.730.273.00
betaCoef0.250.020.27
build_models0.250.000.25
build_study0.280.000.28
deSet0.850.000.84
edge0.010.000.02
endotoxin1.240.041.28
fitFull0.40.00.4
fitNull0.420.020.44
fit_models0.460.000.46
fullMatrix0.410.000.41
fullModel0.680.000.69
gibson1.070.001.06
individual0.380.030.40
kidney1.260.001.27
kl_clust0.490.000.48
lrt0.820.050.88
nullMatrix0.220.030.25
nullModel0.630.000.62
odp1.540.031.58
qvalueObj0.850.030.88
resFull0.280.000.28
resNull0.260.000.27
sType0.390.010.40
show1.310.021.33
summary1.30.01.3

edge.Rcheck/examples_x64/edge-Ex.timings

nameusersystemelapsed
apply_jackstraw1.950.052.00
apply_qvalue0.660.000.66
apply_snm12.84 0.8913.73
apply_sva2.840.163.00
betaCoef0.490.010.50
build_models0.500.020.52
build_study0.440.010.45
deSet0.990.000.99
edge000
endotoxin0.900.020.92
fitFull0.310.000.31
fitNull0.290.000.28
fit_models0.280.020.30
fullMatrix0.280.000.28
fullModel0.450.000.45
gibson0.990.000.99
individual0.450.000.45
kidney1.000.011.02
kl_clust0.50.00.5
lrt0.910.030.94
nullMatrix0.310.000.31
nullModel101
odp1.940.072.00
qvalueObj1.010.001.02
resFull0.340.000.34
resNull0.30.00.3
sType0.310.000.31
show0.830.000.83
summary1.050.001.04