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This page was generated on 2022-04-13 12:06:59 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 NanoStringDiff on tokay2


To the developers/maintainers of the NanoStringDiff package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/NanoStringDiff.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1265/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringDiff 1.24.0  (landing page)
tingting zhai ,hong wang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/NanoStringDiff
git_branch: RELEASE_3_14
git_last_commit: c141f8c
git_last_commit_date: 2021-10-26 12:21:56 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: NanoStringDiff
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoStringDiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NanoStringDiff_1.24.0.tar.gz
StartedAt: 2022-04-12 23:35:54 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:41:33 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 338.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: NanoStringDiff.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoStringDiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NanoStringDiff_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoStringDiff.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NanoStringDiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NanoStringDiff' version '1.24.0'
* 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 'NanoStringDiff' 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
PlotsPositiveHousekeeping: no visible global function definition for
  'read.table'
PlotsPositiveHousekeeping: no visible global function definition for
  'glm'
PlotsPositiveHousekeeping: no visible global function definition for
  'poisson'
PlotsPositiveHousekeeping: no visible global function definition for
  'rowVars'
PlotsPositiveHousekeeping: no visible global function definition for
  'par'
PlotsPositiveHousekeeping: no visible global function definition for
  'abline'
PlotsPositiveHousekeeping: no visible global function definition for
  'lm'
PlotsPositiveHousekeeping: no visible global function definition for
  'title'
PlotsPositiveHousekeeping: no visible global function definition for
  'textxy'
compute.baseSigma: no visible global function definition for 'IQR'
createNanoStringSetFromCsv: no visible global function definition for
  'read.table'
est.dispersion : get.phihat: no visible global function definition for
  'optimize'
estNormalizationFactors: no visible global function definition for
  'glm'
estNormalizationFactors: no visible global function definition for
  'poisson'
estNormalizationFactors: no visible binding for global variable
  'median'
glm.LRT: no visible global function definition for 'pchisq'
glm.LRT: no visible global function definition for 'p.adjust'
glmfit.OneGroup : get.mu: no visible global function definition for
  'optimize'
glmfit.full: no visible global function definition for 'lm'
glmfit.full: no visible global function definition for 'median'
glmfit.full: no visible global function definition for 'IQR'
glmfit.full : get.phi: no visible global function definition for
  'optimize'
glmfit.full : get.beta.full: no visible global function definition for
  'optim'
glmfit.reduce: no visible global function definition for 'lm'
glmfit.reduce : get.beta.reduce: no visible global function definition
  for 'optim'
rnegbinom: no visible global function definition for 'rpois'
rnegbinom: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  IQR abline glm lm median optim optimize p.adjust par pchisq poisson
  read.table rgamma rowVars rpois textxy title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "IQR", "glm", "lm", "median", "optim", "optimize",
             "p.adjust", "pchisq", "poisson", "rgamma", "rpois")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'compute.baseSigma' 'est.dispersion' 'fun5' 'glmfit.OneGroup'
  'glmfit.full' 'glmfit.reduce' 'rnegbinom'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.14-bioc/R/library/NanoStringDiff/libs/i386/NanoStringDiff.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoStringDiff/libs/x64/NanoStringDiff.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 installed files from 'inst/doc' ... NOTE
The following files look like leftovers/mistakes:
  'NanoStringDiff.log'
Please remove them from your package.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
glm.LRT 130.38   0.01  130.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
glm.LRT 133.22   0.02  133.25
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoStringDiff.Rcheck/00check.log'
for details.

Installation output

NanoStringDiff.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/NanoStringDiff_1.24.0.tar.gz && rm -rf NanoStringDiff.buildbin-libdir && mkdir NanoStringDiff.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NanoStringDiff.buildbin-libdir NanoStringDiff_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NanoStringDiff_1.24.0.zip && rm NanoStringDiff_1.24.0.tar.gz NanoStringDiff_1.24.0.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
100  313k  100  313k    0     0   391k      0 --:--:-- --:--:-- --:--:--  391k
100  313k  100  313k    0     0   391k      0 --:--:-- --:--:-- --:--:--  391k

install for i386

* installing *source* package 'NanoStringDiff' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fun5.cpp -o fun5.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o NanoStringDiff.dll tmp.def RcppExports.o fun5.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoStringDiff.buildbin-libdir/00LOCK-NanoStringDiff/00new/NanoStringDiff/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NanoStringDiff'
    finding HTML links ... done
    NanoStringData                          html  
    NanoStringDataNormalization             html  
    NanoStringDiff-class                    html  
    NanoStringDiff-package                  html  
    PlotsPositiveHousekeeping               html  
    estNormalizationFactors                 html  
    glm.LRT                                 html  
    housekeepingControl                     html  
    housekeepingFactor                      html  
    negativeControl                         html  
    negativeFactor                          html  
    positiveControl                         html  
    positiveFactor                          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 'NanoStringDiff' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fun5.cpp -o fun5.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o NanoStringDiff.dll tmp.def RcppExports.o fun5.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoStringDiff.buildbin-libdir/NanoStringDiff/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NanoStringDiff' as NanoStringDiff_1.24.0.zip
* DONE (NanoStringDiff)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'NanoStringDiff' successfully unpacked and MD5 sums checked

Tests output

NanoStringDiff.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(NanoStringDiff)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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("NanoStringDiff")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
   3.03    0.15    3.17

NanoStringDiff.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(NanoStringDiff)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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("NanoStringDiff")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
   2.98    0.10    3.07

Example timings

NanoStringDiff.Rcheck/examples_i386/NanoStringDiff-Ex.timings

nameusersystemelapsed
NanoStringData0.030.000.03
NanoStringDataNormalization000
NanoStringDiff-class0.150.000.16
NanoStringDiff-package000
PlotsPositiveHousekeeping000
estNormalizationFactors0.020.000.02
glm.LRT130.38 0.01130.41
housekeepingControl000
housekeepingFactor0.010.000.01
negativeControl000
negativeFactor000
positiveControl0.000.020.02
positiveFactor000

NanoStringDiff.Rcheck/examples_x64/NanoStringDiff-Ex.timings

nameusersystemelapsed
NanoStringData0.050.000.04
NanoStringDataNormalization000
NanoStringDiff-class0.220.000.22
NanoStringDiff-package000
PlotsPositiveHousekeeping000
estNormalizationFactors0.010.000.01
glm.LRT133.22 0.02133.25
housekeepingControl0.020.000.02
housekeepingFactor000
negativeControl000
negativeFactor0.010.000.02
positiveControl000
positiveFactor000