| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:38 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the GeomxTools package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 767/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeomxTools 2.0.0 (landing page) Nicole Ortogero
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeomxTools |
| Version: 2.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeomxTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeomxTools_2.0.0.tar.gz |
| StartedAt: 2022-04-12 20:24:32 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:46:16 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1303.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeomxTools.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeomxTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeomxTools_2.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeomxTools.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeomxTools/DESCRIPTION' ... OK
* this is package 'GeomxTools' version '2.0.0'
* 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 whether package 'GeomxTools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.7Mb
sub-directories of 1Mb or more:
extdata 11.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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
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'
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 TargetName assayDataElement2 setSigFuncs<-
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readNanoStringGeoMxSet 40.31 0.75 41.06
setBioProbeQCFlags 34.70 0.03 34.74
setQCFlags-NanoStringGeoMxSet-method 32.41 0.05 32.46
NanoStringGeoMxSet-class 19.92 0.53 30.39
writeNanoStringGeoMxSet 14.83 0.35 19.89
aggregateCounts 14.41 0.15 15.13
mixedModelDE 14.27 0.05 35.24
readDccFile 6.33 0.08 6.41
readPKCFile 5.91 0.04 5.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
setQCFlags-NanoStringGeoMxSet-method 42.57 0.03 42.61
setBioProbeQCFlags 41.76 0.02 41.79
readNanoStringGeoMxSet 40.05 0.78 40.83
NanoStringGeoMxSet-class 17.89 0.35 20.86
writeNanoStringGeoMxSet 17.92 0.23 21.34
aggregateCounts 15.97 0.09 16.08
mixedModelDE 14.78 0.10 39.75
readPKCFile 5.59 0.05 5.64
readDccFile 5.27 0.03 5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeomxTools.Rcheck/00check.log'
for details.
GeomxTools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GeomxTools_2.0.0.tar.gz && rm -rf GeomxTools.buildbin-libdir && mkdir GeomxTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeomxTools.buildbin-libdir GeomxTools_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeomxTools_2.0.0.zip && rm GeomxTools_2.0.0.tar.gz GeomxTools_2.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
3 4261k 3 135k 0 0 321k 0 0:00:13 --:--:-- 0:00:13 321k
31 4261k 31 1344k 0 0 946k 0 0:00:04 0:00:01 0:00:03 946k
76 4261k 76 3274k 0 0 1360k 0 0:00:03 0:00:02 0:00:01 1360k
100 4261k 100 4261k 0 0 1553k 0 0:00:02 0:00:02 --:--:-- 1553k
install for i386
* installing *source* package 'GeomxTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeomxTools'
finding HTML links ... done
NanoStringGeoMxSet-class html
finding level-2 HTML links ... done
aggregateCounts html
checkQCFlags-NanoStringGeoMxSet-method
html
checkQCFlags html
countsShiftedByOne html
logtBase html
mixedModelDE html
ngeoMean html
ngeoSD html
normalize-NanoStringGeoMxSet-method html
readDccFile html
readNanoStringGeoMxSet html
readPKCFile html
setBackgroundQCFlags html
setBioProbeQCFlags html
setGeoMxQCFlags html
setQCFlags-NanoStringGeoMxSet-method html
setSegmentQCFlags html
setSeqQCFlags html
shiftCountsOne html
summarizeNegatives html
writeNanoStringGeoMxSet html
** 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
install for x64
* installing *source* package 'GeomxTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeomxTools' as GeomxTools_2.0.0.zip
* DONE (GeomxTools)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GeomxTools' successfully unpacked and MD5 sums checked
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GeomxTools.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ggplot2
>
> 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
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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
>
> proc.time()
user system elapsed
299.56 2.32 336.48
|
GeomxTools.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> 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, 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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ggplot2
>
> 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
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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
>
> proc.time()
user system elapsed
319.26 1.71 321.03
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GeomxTools.Rcheck/examples_i386/GeomxTools-Ex.timings
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GeomxTools.Rcheck/examples_x64/GeomxTools-Ex.timings
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