| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:03 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1386/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoStringNCTools 1.10.1 (landing page) Nicole Ortogero
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the NanoStringNCTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoStringNCTools.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: NanoStringNCTools |
| Version: 1.10.1 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringNCTools.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.10.1.tar.gz |
| StartedAt: 2024-04-16 03:11:47 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:14:00 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 132.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NanoStringNCTools.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringNCTools.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.10.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/NanoStringNCTools.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'NanoStringNCTools/DESCRIPTION' ... OK
* this is package 'NanoStringNCTools' version '1.10.1'
* package encoding: UTF-8
* 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 'NanoStringNCTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
autoplot.NanoStringRccSet : <anonymous>: warning in switch(x[2], A =
qcCutoffs[["BindingDensity"]][["maximumBD"]], B =
qcCutoffs[["BindingDensity"]][["maximumBD"]], C =
qcCutoffs[["BindingDensity"]][["maximumBD"]], D =
qcCutoffs[["BindingDensity"]][["maximumBD"]], E =
qcCutoffs[["BindingDensity"]][["maximumBD"]], G =
qcCutoffs[["BindingDensity"]][["maximumBD"]], H =
qcCutoffs[["BindingDensity"]][["maximumBD"]], P =
qcCutoffs[["BindingDensity"]][["maximumBDSprint"]], default =
qcCutoffs[["BindingDensity"]][["maximumBD"]]): partial argument match
of 'E' to 'EXPR'
setQCFlags,NanoStringRccSet : <anonymous>: warning in switch(x[2], A =
maxBindDen, B = maxBindDen, C = maxBindDen, D = maxBindDen, E =
maxBindDen, G = maxBindDen, H = maxBindDen, P = maxBindDenSprint,
default = maxBindDen): partial argument match of 'E' to 'EXPR'
autoplot.NanoStringRccSet: no visible binding for global variable
'xend'
autoplot.NanoStringRccSet: no visible binding for global variable
'passingThreshold'
autoplot.NanoStringRccSet: no visible binding for global variable
'GeomMean'
autoplot.NanoStringRccSet: no visible binding for global variable 'h'
autoplot.NanoStringRccSet: no visible binding for global variable
'label'
Undefined global functions or variables:
GeomMean h label passingThreshold xend
* checking Rd files ... WARNING
checkRd: (5) NanoStringRccSet-class.Rd:147-150: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:163-166: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:167-170: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:171-174: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:175-179: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:180-184: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:185-187: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:188-190: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:191-193: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:194-196: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:202-221: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:229-236: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:237-241: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:242-246: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:247-251: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:252-256: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:257-261: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:262-266: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:267-271: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:277-281: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:282-286: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:287-292: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:298-303: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:304-312: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:318-324: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:330-332: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:338-341: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:342-344: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:65-67: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:68-71: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:76-79: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:80-83: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:84-86: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:87-89: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:90-93: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:94-96: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:97-99: \item in \describe must have non-empty label
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'run_unitTests.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
'F:/biocbuild/bbs-3.18-bioc/meat/NanoStringNCTools.Rcheck/00check.log'
for details.
NanoStringNCTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL NanoStringNCTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'NanoStringNCTools' ... ** using staged installation ** R ** 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 (NanoStringNCTools)
NanoStringNCTools.Rcheck/tests/run_unitTests.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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.
> require("NanoStringNCTools") || stop("unable to load NanoStringNCTools package")
Loading required package: NanoStringNCTools
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, 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")'.
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ggplot2
[1] TRUE
> BiocGenerics:::testPackage("NanoStringNCTools")
RUNIT TEST PROTOCOL -- Tue Apr 16 03:13:48 2024
***********************************************
Number of test functions: 52
Number of errors: 0
Number of failures: 0
1 Test Suite :
NanoStringNCTools RUnit Tests - 52 test functions, 0 errors, 0 failures
Number of test functions: 52
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.56 0.42 12.95
NanoStringNCTools.Rcheck/NanoStringNCTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringRccSet-autoplot | 0.43 | 0.03 | 0.47 | |
| NanoStringRccSet-class | 1.47 | 0.18 | 1.64 | |
| SignatureSet | 0.05 | 0.00 | 0.05 | |
| geom_beeswarm_interactive | 0.37 | 0.00 | 0.37 | |
| log2t | 0 | 0 | 0 | |
| normalize | 0.22 | 0.01 | 0.23 | |
| readNanoStringRccSet | 0.76 | 0.03 | 0.82 | |
| readRccFile | 0.07 | 0.00 | 0.06 | |
| readRlfFile | 0.03 | 0.00 | 0.03 | |
| sScale | 0.00 | 0.02 | 0.03 | |
| setQCFlags | 0.69 | 0.01 | 0.71 | |
| writeNanoStringRccSet | 0.50 | 0.02 | 0.51 | |