| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:32 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 GeomxTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeomxTools.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 811/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeomxTools 3.5.0 (landing page) Nicole Ortogero
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: GeomxTools |
| Version: 3.5.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GeomxTools_3.5.0.tar.gz |
| StartedAt: 2023-06-05 23:10:43 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 23:43:25 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 1961.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeomxTools.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GeomxTools_3.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GeomxTools.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.5.0’
* 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 ‘GeomxTools’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.3Mb
sub-directories of 1Mb or more:
extdata 18.4Mb
* 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 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
aggregateCounts: no visible binding for global variable ‘TargetName’
hkNorm: no visible binding for global variable ‘TargetName’
mixedModelDE: multiple local function definitions for ‘deFunc’ with
different formal arguments
qgrubbs: no visible global function definition for ‘qtable’
readPKCFile: no visible binding for global variable ‘RTS_ID’
readPKCFile: no visible binding for global variable ‘Module’
setGrubbsFlags: no visible binding for global variable ‘TargetName’
setGrubbsFlags : <anonymous>: no visible binding for global variable
‘Module’
setProbeRatioFlags: no visible binding for global variable ‘TargetName’
setTargetFlags: no visible global function definition for ‘analtye’
subtractBackground : <anonymous>: no visible binding for global
variable ‘Module’
setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global
function definition for ‘setSigFuncs<-’
signatureScores,NanoStringGeoMxSet: no visible global function
definition for ‘assayDataElement2’
signatureScores,NanoStringGeoMxSet: no visible global function
definition for ‘.sigCalc’
Undefined global functions or variables:
.sigCalc Module RTS_ID TargetName analtye assayDataElement2 qtable
setSigFuncs<-
* checking Rd files ... WARNING
checkRd: (5) NanoStringGeoMxSet-class.Rd:109-112: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:113-116: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:117-120: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:121-124: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:125-128: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:129-132: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:133-136: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:141-144: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:145-149: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:150-154: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:163-166: \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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mixedModelDE 92.590 1.909 97.634
normalize-NanoStringGeoMxSet-method 74.689 2.100 0.122
readNanoStringGeoMxSet 64.096 1.440 65.734
NanoStringGeoMxSet-class 24.484 0.395 25.030
writeNanoStringGeoMxSet 21.645 0.199 21.916
setQCFlags-NanoStringGeoMxSet-method 21.126 0.115 21.304
setBioProbeQCFlags 20.814 0.172 21.051
aggregateCounts 17.007 0.196 17.241
readPKCFile 12.759 0.179 12.975
as.SpatialExperiment 9.078 0.147 9.249
plotConcordance 6.026 0.722 6.771
* 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 ...
‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using ‘UTF-8’... OK
‘GeomxSet_coercions.Rmd’ using ‘UTF-8’... OK
‘Protein_in_GeomxTools.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/GeomxTools.Rcheck/00check.log’
for details.
GeomxTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL GeomxTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘GeomxTools’ ... ** 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 (GeomxTools)
GeomxTools.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(GeomxTools)
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: NanoStringNCTools
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
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
>
> test_check("GeomxTools")
Attaching package: 'EnvStats'
The following objects are masked from 'package:stats':
predict, predict.lm
The following object is masked from 'package:base':
print.default
Attaching SeuratObject
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:EnvStats':
iqr
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeuratObject':
Assays
The following object is masked from 'package:Seurat':
Assays
Attaching package: 'SingleCellExperiment'
The following object is masked from 'package:NanoStringNCTools':
weights<-
Loading required package: lme4
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'lmerTest'
The following object is masked from 'package:lme4':
lmer
The following object is masked from 'package:stats':
step
boundary (singular) fit: see help('isSingular')
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 290 ]
>
> proc.time()
user system elapsed
888.695 10.436 933.936
GeomxTools.Rcheck/GeomxTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringGeoMxSet-class | 24.484 | 0.395 | 25.030 | |
| aggregateCounts | 17.007 | 0.196 | 17.241 | |
| as.Seurat | 4.654 | 0.076 | 4.740 | |
| as.SpatialExperiment | 9.078 | 0.147 | 9.249 | |
| checkQCFlags-NanoStringGeoMxSet-method | 0.06 | 0.00 | 0.06 | |
| checkQCFlags | 0.082 | 0.000 | 0.083 | |
| computeNormalizationFactors | 0.021 | 0.000 | 0.022 | |
| countsShiftedByOne | 0.055 | 0.004 | 0.059 | |
| logtBase | 0 | 0 | 0 | |
| mixedModelDE | 92.590 | 1.909 | 97.634 | |
| ngeoMean | 0 | 0 | 0 | |
| ngeoSD | 0.000 | 0.000 | 0.001 | |
| normalize-NanoStringGeoMxSet-method | 74.689 | 2.100 | 0.122 | |
| plotConcordance | 6.026 | 0.722 | 6.771 | |
| plotNormFactorConcordance | 3.429 | 0.200 | 3.639 | |
| qcProteinSignal | 0.224 | 0.000 | 0.224 | |
| qcProteinSignalNames | 0.018 | 0.000 | 0.018 | |
| readDccFile | 0.438 | 0.016 | 0.455 | |
| readNanoStringGeoMxSet | 64.096 | 1.440 | 65.734 | |
| readPKCFile | 12.759 | 0.179 | 12.975 | |
| setBackgroundQCFlags | 0.140 | 0.004 | 0.145 | |
| setBioProbeQCFlags | 20.814 | 0.172 | 21.051 | |
| setGeoMxQCFlags | 0.085 | 0.000 | 0.084 | |
| setQCFlags-NanoStringGeoMxSet-method | 21.126 | 0.115 | 21.304 | |
| setSegmentQCFlags | 0.184 | 0.004 | 0.188 | |
| setSeqQCFlags | 0.119 | 0.000 | 0.119 | |
| shiftCountsOne | 0.085 | 0.004 | 0.090 | |
| summarizeNegatives | 1.016 | 0.008 | 1.027 | |
| writeNanoStringGeoMxSet | 21.645 | 0.199 | 21.916 | |