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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the NanoStringDiff package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1245/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoStringDiff 1.22.0 (landing page) tingting zhai
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: NanoStringDiff |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoStringDiff_1.22.0.tar.gz |
| StartedAt: 2021-10-14 21:38:46 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:41:15 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 149.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NanoStringDiff.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoStringDiff_1.22.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/NanoStringDiff.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoStringDiff’ version ‘1.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 is not available
* 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 95.978 1.516 97.552
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/NanoStringDiff.Rcheck/00check.log’
for details.
NanoStringDiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NanoStringDiff ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘NanoStringDiff’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fun5.cpp -o fun5.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o NanoStringDiff.so RcppExports.o fun5.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-NanoStringDiff/00new/NanoStringDiff/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (NanoStringDiff)
NanoStringDiff.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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, 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
2.809 0.153 2.942
NanoStringDiff.Rcheck/NanoStringDiff-Ex.timings
| name | user | system | elapsed | |
| NanoStringData | 0.023 | 0.006 | 0.028 | |
| NanoStringDataNormalization | 0 | 0 | 0 | |
| NanoStringDiff-class | 0.205 | 0.008 | 0.213 | |
| NanoStringDiff-package | 0.000 | 0.001 | 0.001 | |
| PlotsPositiveHousekeeping | 0 | 0 | 0 | |
| estNormalizationFactors | 0.021 | 0.002 | 0.023 | |
| glm.LRT | 95.978 | 1.516 | 97.552 | |
| housekeepingControl | 0.005 | 0.003 | 0.007 | |
| housekeepingFactor | 0.002 | 0.002 | 0.004 | |
| negativeControl | 0.002 | 0.002 | 0.003 | |
| negativeFactor | 0.003 | 0.002 | 0.005 | |
| positiveControl | 0.003 | 0.003 | 0.006 | |
| positiveFactor | 0.002 | 0.001 | 0.004 | |