Robert Ziman
| Snapshot Date: 2023-04-19 23:55:56 -0400 (Wed, 19 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/NanoStringQCPro |
| git_branch: devel |
| git_last_commit: 7fe4f04 |
| git_last_commit_date: 2023-03-14 11:46:52 -0400 (Tue, 14 Mar 2023) |
| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-04-20 12:50:32 -0400 (Thu, 20 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-04-19 r84288) -- "Unsuffered Consequences" | 3941 |
| 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 | ||||
|
To the developers/maintainers of the NanoStringQCPro package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoStringQCPro.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1353/2223 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Robert Ziman
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| Package: NanoStringQCPro |
| Version: 1.31.1 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings NanoStringQCPro_1.31.1.tar.gz |
| StartedAt: 2023-04-20 08:24:54 -0400 (Thu, 20 Apr 2023) |
| EndedAt: 2023-04-20 08:27:08 -0400 (Thu, 20 Apr 2023) |
| EllapsedTime: 133.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NanoStringQCPro.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings NanoStringQCPro_1.31.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/NanoStringQCPro.Rcheck’
* using R Under development (unstable) (2023-04-19 r84288)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘NanoStringQCPro/DESCRIPTION’ ... OK
* this is package ‘NanoStringQCPro’ version ‘1.31.1’
* 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 ‘NanoStringQCPro’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'NanoStringQCPro' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.18-bioc/meat/NanoStringQCPro.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘knitr’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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
centeredSampleClustering: no visible global function definition for
‘png’
centeredSampleClustering: no visible global function definition for
‘dev.off’
countsInBlankSamples_verticalPlot: no visible global function
definition for ‘png’
countsInBlankSamples_verticalPlot: no visible global function
definition for ‘dev.off’
geneClustering: no visible global function definition for ‘png’
geneClustering: no visible global function definition for ‘dev.off’
negCtrlsByLane_verticalPlot: no visible global function definition for
‘png’
negCtrlsByLane_verticalPlot: no visible global function definition for
‘dev.off’
previewPNG: no visible global function definition for ‘png’
previewPNG: no visible global function definition for ‘dev.off’
sampleClustering,RccSet: no visible global function definition for
‘png’
sampleClustering,RccSet: no visible global function definition for
‘dev.off’
Undefined global functions or variables:
dev.off png
Consider adding
importFrom("grDevices", "dev.off", "png")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/NanoStringQCPro.Rcheck/00check.log’
for details.
NanoStringQCPro.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL NanoStringQCPro ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘NanoStringQCPro’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’ Warning: Package 'NanoStringQCPro' is deprecated and will be removed from Bioconductor version 3.18 ** testing if installed package can be loaded from final location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’ Warning: Package 'NanoStringQCPro' is deprecated and will be removed from Bioconductor version 3.18 ** testing if installed package keeps a record of temporary installation path * DONE (NanoStringQCPro)
NanoStringQCPro.Rcheck/NanoStringQCPro-Ex.timings
| name | user | system | elapsed | |
| RccSet-class | 0.366 | 0.000 | 0.366 | |
| addCodesetAnnotation | 0.176 | 0.012 | 0.189 | |
| buildCodesetAnnotation | 0.009 | 0.000 | 0.009 | |
| checkRccSet | 0.055 | 0.003 | 0.059 | |
| contentNorm | 0.093 | 0.004 | 0.097 | |
| copyRccSet | 0.009 | 0.005 | 0.013 | |
| getBackground | 0.062 | 0.004 | 0.066 | |
| getBlankLabel | 0.002 | 0.000 | 0.001 | |
| makeQCReport | 3.323 | 0.304 | 3.595 | |
| newRccSet | 0.181 | 0.000 | 0.180 | |
| posCtrlNorm | 0.015 | 0.000 | 0.015 | |
| preprocRccSet | 0.111 | 0.000 | 0.111 | |
| presAbsCall | 0.036 | 0.004 | 0.040 | |
| readCdrDesignData | 0.002 | 0.000 | 0.002 | |
| readRcc | 0.000 | 0.003 | 0.003 | |
| readRlf | 0.003 | 0.000 | 0.003 | |
| subtractBackground | 0.058 | 0.000 | 0.058 | |