Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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

Package 1366/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringDiff 1.35.0  (landing page)
tingting zhai ,hong wang
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/NanoStringDiff
git_branch: devel
git_last_commit: b3fd0a0
git_last_commit_date: 2024-04-30 10:45:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for NanoStringDiff on palomino6

To the developers/maintainers of the NanoStringDiff package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoStringDiff.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NanoStringDiff
Version: 1.35.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringDiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings NanoStringDiff_1.35.0.tar.gz
StartedAt: 2024-07-16 02:13:39 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 02:16:47 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 188.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: NanoStringDiff.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringDiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings NanoStringDiff_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/NanoStringDiff.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'NanoStringDiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NanoStringDiff' version '1.35.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
Auto-generated content requiring editing in Rd file 'NanoStringDiff-package.Rd':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
* 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 x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/NanoStringDiff/libs/x64/NanoStringDiff.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
glm.LRT 137.73   2.57  139.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/NanoStringDiff.Rcheck/00check.log'
for details.


Installation output

NanoStringDiff.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL NanoStringDiff
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'NanoStringDiff' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fun5.cpp -o fun5.o
g++ -std=gnu++17 -shared -s -static-libgcc -o NanoStringDiff.dll tmp.def RcppExports.o fun5.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-NanoStringDiff/00new/NanoStringDiff/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (NanoStringDiff)

Tests output

NanoStringDiff.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, aperm, 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, 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 
   2.34    0.18    2.51 

Example timings

NanoStringDiff.Rcheck/NanoStringDiff-Ex.timings

nameusersystemelapsed
NanoStringData0.020.000.01
NanoStringDataNormalization000
NanoStringDiff-class0.140.010.15
NanoStringDiff-package000
PlotsPositiveHousekeeping000
estNormalizationFactors0.020.000.02
glm.LRT137.73 2.57139.16
housekeepingControl0.020.000.01
housekeepingFactor000
negativeControl000
negativeFactor000
positiveControl000
positiveFactor0.000.010.01