| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1355/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoStringNCTools 1.8.0 (landing page) Nicole Ortogero
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the NanoStringNCTools package: - 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: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringNCTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringNCTools_1.8.0.tar.gz |
| StartedAt: 2023-10-18 10:52:47 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 10:56:13 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 206.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NanoStringNCTools.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringNCTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringNCTools_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NanoStringNCTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringNCTools/DESCRIPTION’ ... OK
* this is package ‘NanoStringNCTools’ version ‘1.8.0’
* 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 for sufficient/correct file permissions ... 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
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NanoStringNCTools.Rcheck/00check.log’
for details.
NanoStringNCTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoStringNCTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 -- Wed Oct 18 10:55:54 2023
***********************************************
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
12.690 0.413 20.166
NanoStringNCTools.Rcheck/NanoStringNCTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringRccSet-autoplot | 0.473 | 0.021 | 0.752 | |
| NanoStringRccSet-class | 1.163 | 0.151 | 2.026 | |
| SignatureSet | 0.029 | 0.001 | 0.043 | |
| geom_beeswarm_interactive | 0.357 | 0.009 | 0.559 | |
| log2t | 0.001 | 0.000 | 0.000 | |
| normalize | 0.305 | 0.007 | 0.479 | |
| readNanoStringRccSet | 0.949 | 0.020 | 1.479 | |
| readRccFile | 0.069 | 0.004 | 0.110 | |
| readRlfFile | 0.055 | 0.002 | 0.086 | |
| sScale | 0.004 | 0.001 | 0.007 | |
| setQCFlags | 0.61 | 0.01 | 0.95 | |
| writeNanoStringRccSet | 0.461 | 0.020 | 0.733 | |