Agnes Paquet
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/arrayQuality |
| git_branch: RELEASE_3_13 |
| git_last_commit: f319a3a |
| git_last_commit_date: 2021-05-19 11:34:12 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:57 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the arrayQuality package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/arrayQuality.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 84/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| arrayQuality 1.70.0 (landing page) Agnes Paquet
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: arrayQuality |
| Version: 1.70.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:arrayQuality.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings arrayQuality_1.70.0.tar.gz |
| StartedAt: 2021-10-14 19:37:22 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:38:26 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 64.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: arrayQuality.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:arrayQuality.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings arrayQuality_1.70.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/arrayQuality.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.70.0'
* 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 'arrayQuality' can be installed ... OK
* checking installed package size ... NOTE
installed size is 44.9Mb
sub-directories of 1Mb or more:
Heebo 17.1Mb
Meebo 12.2Mb
gprQCData 14.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 ... NOTE
'library' or 'require' calls in package code:
'HEEBOdata' 'MEEBOdata' 'mclust'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PRv9mers: warning in layout(matrix(c(7, 1, 2, 7, 3, 3, 7, 4, 4, 7, 5,
6), 3, 4), height = c(0.5, 4, 4), width = c(12, 5, 2, 7)): partial
argument match of 'width' to 'widths'
PRv9mers: warning in layout(matrix(c(7, 1, 2, 7, 3, 3, 7, 4, 4, 7, 5,
6), 3, 4), height = c(0.5, 4, 4), width = c(12, 5, 2, 7)): partial
argument match of 'height' to 'heights'
PRvQCHyb: warning in layout(matrix(c(11, 1, 1, 2, 11, 3, 3, 7, 11, 4,
4, 7, 11, 5, 5, 7, 11, 6, 6, 7, 11, 8, 9, 10), 4, 6), height = c(0.5,
2, 2, 4), width = c(12, 5.5, 2, 5.5, 2, 7)): partial argument match
of 'width' to 'widths'
PRvQCHyb: warning in layout(matrix(c(11, 1, 1, 2, 11, 3, 3, 7, 11, 4,
4, 7, 11, 5, 5, 7, 11, 6, 6, 7, 11, 8, 9, 10), 4, 6), height = c(0.5,
2, 2, 4), width = c(12, 5.5, 2, 5.5, 2, 7)): partial argument match
of 'height' to 'heights'
PRvQCHyb: warning in qpDotPlots(mraw, x = "maA", col = colcode):
partial argument match of 'x' to 'xvar'
PRvQCHyb: warning in qpDotPlots(mraw, x = "maA", col = colcode):
partial argument match of 'col' to 'colcode'
heeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
7)): partial argument match of 'width' to 'widths'
heeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
7)): partial argument match of 'height' to 'heights'
heeboQualityPlots: warning in qpBoxplotMeebo(mraw, xvar = "maA", col =
colcode, main = "Control A", cex.main = 0.8, id = controlId,
meeboAnnot = HEEBOset): partial argument match of 'col' to 'colcode'
heeboQualityPlots: warning in qpDotPlotsEEBO(mraw, xvar = "maM", col =
colcode, main = "Control M", cex.main = 0.8, id = seqId, meeboAnnot =
HEEBOset): partial argument match of 'col' to 'colcode'
maQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
7)): partial argument match of 'width' to 'widths'
maQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
7)): partial argument match of 'height' to 'heights'
maQualityPlots: warning in qpDotPlots(mnorm, xvar = "maM", col =
colcode, main = "Control normalized M", cex.main = 0.8, id =
controlId): partial argument match of 'col' to 'colcode'
maQualityPlots: warning in qpDotPlots(mraw, xvar = "maA", col =
colcode, main = "Control A", cex.main = 0.8, id = controlId): partial
argument match of 'col' to 'colcode'
meeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
7)): partial argument match of 'width' to 'widths'
meeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
7)): partial argument match of 'height' to 'heights'
meeboQualityPlots: warning in qpBoxplotMeebo(mraw, xvar = "maA", col =
colcode, main = "Control A", cex.main = 0.8, id = controlId,
meeboAnnot = MEEBOset): partial argument match of 'col' to 'colcode'
meeboQualityPlots: warning in qpDotPlotsEEBO(mraw, xvar = "maM", col =
colcode, main = "Control M", cex.main = 0.8, id = seqId, meeboAnnot =
MEEBOset): partial argument match of 'col' to 'colcode'
qpBEplot.linear: warning in axis(1, at = seq(-50, 120, 10), label =
seq(50, -120, -10)): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(1, at = seq(0, 90, 10), label = seq(0,
90, 10)): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(1, at = c(-10, 100), label = c("WT",
"Neg ctl")): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(4, at =
quantile(mnorm$A[coreCollection, 1], c(0.25, 0.75, 0.9, 1), na.rm =
TRUE), label = c(0.25, 0.75, 0.9, 1), las = 2): partial argument
match of 'label' to 'labels'
qpTiling: warning in axis(1, at = unique(sort(-as.numeric(distance))),
label = rev(unique(sort(as.numeric(distance))))): partial argument
match of 'label' to 'labels'
EMSplit : meV.na: no visible global function definition for 'me'
PRvQCHyb: no visible binding for global variable 'MmDEGenes'
Spike.Cy5vsCy3: no visible binding for global variable 'MEEBOset'
Spike.Cy5vsCy3: no visible binding for global variable 'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
'MEEBOset'
Spike.Individual.Sensitivity: no visible binding for global variable
'MEEBOctrl'
Spike.MM.Scatter: no visible binding for global variable 'RG'
Spike.MM.Scatter: no visible binding for global variable 'MEEBOset'
Spike.MMplot: no visible binding for global variable 'RG'
Spike.MMplot: no visible binding for global variable 'MEEBOset'
Spike.Sensitivity: no visible binding for global variable 'RG'
Spike.Sensitivity: no visible binding for global variable 'MEEBOset'
arrayScal: no visible binding for global variable 'MmReferenceDB'
getSpikeIds: no visible binding for global variable 'MEEBOset'
getSpikeIndex: no visible binding for global variable 'MEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOctrl'
heeboQuality: no visible binding for global variable 'HEEBOtilingres'
heeboQualityPlots: no visible binding for global variable 'HEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOctrl'
meeboQuality: no visible binding for global variable 'MEEBOtilingres'
meeboQualityPlots: no visible binding for global variable 'MEEBOset'
qpBEplot.linear: no visible binding for global variable 'MEEBOctrl'
qpBoxplotMeebo: no visible binding for global variable 'MEEBOset'
qpDotPlotsEEBO: no visible binding for global variable 'MEEBOset'
qpDotPlotsMeebo: no visible binding for global variable 'MEEBOset'
qpMisMatchPlot: no visible binding for global variable 'HEEBOctrl'
qpTiling: no visible binding for global variable 'MEEBOtilingres'
qualBoxplot: no visible binding for global variable 'MmReferenceDB'
qualBoxplot: no visible binding for global variable 'HsReferenceDB'
qualityScore: no visible binding for global variable 'MmReferenceDB'
readAllSpikes: no visible binding for global variable 'MEEBOset'
scaleRefTable: no visible binding for global variable 'MmReferenceDB'
Undefined global functions or variables:
HEEBOctrl HEEBOset HEEBOtilingres HsReferenceDB MEEBOctrl MEEBOset
MEEBOtilingres MmDEGenes MmReferenceDB RG me
* checking Rd files ... NOTE
prepare_Rd: spotQuality.Rd:92-93: Dropping empty section \examples
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
'basicQuality.html', 'customQuality.html',
'images/9mersDiagnosticPlot.png', 'images/QCHybDiagPlot.png',
'images/comparativeBoxplot.png', 'images/genHybDiagPlot.png',
'images/htmlReport.png', 'images/lifecycle.png',
'images/mySpotTypes.png', 'images/qualityDiagram.png',
'index.html', 'meeboQualityGuide.htm',
'meeboQualityGuide_files/filelist.xml',
'meeboQualityGuide_files/header.htm',
'meeboQualityGuide_files/image001.jpg',
'meeboQualityGuide_files/image003.jpg',
'meeboQualityGuide_files/image005.png',
'meeboQualityGuide_files/image007.png',
'meeboQualityGuide_files/image009.png',
'meeboQualityGuide_files/image011.png',
'meeboQualityGuide_files/image013.png',
'meeboQualityGuide_files/image015.png',
'meeboQualityGuide_files/image017.png',
'meeboQualityGuide_files/image019.png',
'meeboQualityGuide_files/image021.png', 'print-runQC.html'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/arrayQuality.Rcheck/00check.log'
for details.
arrayQuality.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/arrayQuality_1.70.0.tar.gz && rm -rf arrayQuality.buildbin-libdir && mkdir arrayQuality.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=arrayQuality.buildbin-libdir arrayQuality_1.70.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL arrayQuality_1.70.0.zip && rm arrayQuality_1.70.0.tar.gz arrayQuality_1.70.0.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
21 12.9M 21 2825k 0 0 5044k 0 0:00:02 --:--:-- 0:00:02 5045k
93 12.9M 93 12.1M 0 0 7985k 0 0:00:01 0:00:01 --:--:-- 7985k
100 12.9M 100 12.9M 0 0 8086k 0 0:00:01 0:00:01 --:--:-- 8084k
install for i386
* installing *source* package 'arrayQuality' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'arrayQuality'
finding HTML links ... done
MmDEGenes html
PRv9mers html
PRvQCHyb html
agQuality html
arrayQuality-internal html
globalQuality html
gpQuality html
gprDB html
heeboQuality html
heeboQualityPlots html
maQualityPlots html
meeboQuality html
meeboQualityPlots html
prdata html
qcScore html
qualBoxplot html
qualityScore html
readAgilent html
readGPR html
readSpikeTypes html
readSpot html
readcontrolCode html
scaleRefTable html
slideQuality html
spotQuality 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 'arrayQuality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'arrayQuality' as arrayQuality_1.70.0.zip
* DONE (arrayQuality)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'arrayQuality' successfully unpacked and MD5 sums checked
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arrayQuality.Rcheck/examples_i386/arrayQuality-Ex.timings
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arrayQuality.Rcheck/examples_x64/arrayQuality-Ex.timings
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