Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1391/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoStringDiff 1.36.0 (landing page) tingting zhai
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: NanoStringDiff |
Version: 1.36.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NanoStringDiff_1.36.0.tar.gz |
StartedAt: 2024-12-20 03:28:58 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:34:36 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 338.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: NanoStringDiff.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NanoStringDiff_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/NanoStringDiff.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘NanoStringDiff/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoStringDiff’ version ‘1.36.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 for sufficient/correct file permissions ... OK * checking whether package ‘NanoStringDiff’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... 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 is not available * 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 78.546 0.055 78.604 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/NanoStringDiff.Rcheck/00check.log’ for details.
NanoStringDiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL NanoStringDiff ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘NanoStringDiff’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c fun5.cpp -o fun5.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o NanoStringDiff.so RcppExports.o fun5.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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, saveRDS, 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 1.943 0.088 2.019
NanoStringDiff.Rcheck/NanoStringDiff-Ex.timings
name | user | system | elapsed | |
NanoStringData | 0.015 | 0.004 | 0.020 | |
NanoStringDataNormalization | 0 | 0 | 0 | |
NanoStringDiff-class | 0.141 | 0.006 | 0.148 | |
NanoStringDiff-package | 0 | 0 | 0 | |
PlotsPositiveHousekeeping | 0 | 0 | 0 | |
estNormalizationFactors | 0.011 | 0.000 | 0.011 | |
glm.LRT | 78.546 | 0.055 | 78.604 | |
housekeepingControl | 0.001 | 0.001 | 0.002 | |
housekeepingFactor | 0.002 | 0.000 | 0.001 | |
negativeControl | 0.002 | 0.000 | 0.001 | |
negativeFactor | 0.001 | 0.001 | 0.002 | |
positiveControl | 0.000 | 0.001 | 0.002 | |
positiveFactor | 0.000 | 0.001 | 0.001 | |