Wentao Yang
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ABSSeq |
| git_branch: RELEASE_3_17 |
| git_last_commit: 5e7de8c |
| git_last_commit_date: 2023-04-25 10:31:15 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:57 -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 9/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ABSSeq 1.54.0 (landing page) Wentao Yang
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the ABSSeq 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: ABSSeq |
| Version: 1.54.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ABSSeq_1.54.0.tar.gz |
| StartedAt: 2023-10-17 01:07:30 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 01:10:47 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 196.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ABSSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ABSSeq_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ABSSeq.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 ‘ABSSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ABSSeq’ version ‘1.54.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ABSSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
* 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' call to ‘edgeR’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ABSDataSet: no visible global function definition for ‘new’
ABSSeqlm: no visible global function definition for ‘pnorm’
ABSSeqlm: no visible global function definition for ‘p.adjust’
ReplaceOutliersByMAD: no visible global function definition for ‘is’
ReplaceOutliersByMAD: no visible global function definition for
‘model.matrix’
ReplaceOutliersByMAD: no visible global function definition for
‘predict’
aFoldcomplexDesign: no visible binding for global variable ‘sd’
aFoldcomplexDesign: no visible binding for global variable ‘var’
aFoldcomplexDesign: no visible global function definition for ‘sd’
callDEs: no visible global function definition for ‘is’
callDEs: no visible binding for global variable ‘p.adjust.methods’
callDEs: no visible global function definition for ‘pnorm’
callDEs: no visible global function definition for ‘pnbinom’
callDEs: no visible global function definition for ‘p.adjust’
callParameter: no visible global function definition for ‘is’
callParameter: no visible binding for global variable ‘var’
callParameter: no visible global function definition for ‘quantile’
callParameter: no visible global function definition for ‘predict’
callParameter: no visible global function definition for ‘model.matrix’
callParameterwithoutReplicates: no visible global function definition
for ‘is’
callParameterwithoutReplicates: no visible binding for global variable
‘sd’
callParameterwithoutReplicates: no visible global function definition
for ‘predict’
callParameterwithoutReplicates: no visible binding for global variable
‘var’
callParameterwithoutReplicates: no visible global function definition
for ‘quantile’
callParameterwithoutReplicates: no visible global function definition
for ‘model.matrix’
callPergroup: no visible binding for global variable ‘var’
estimateSizeFactorsForMatrix: no visible binding for global variable
‘median’
genAFold: no visible binding for global variable ‘var’
genAFold: no visible binding for global variable ‘sd’
genAFold: no visible global function definition for ‘sd’
normalFactors: no visible global function definition for ‘is’
normalFactors: no visible global function definition for ‘validObject’
normalFactors : rowQuar: no visible global function definition for
‘quantile’
normalFactors: no visible global function definition for
‘calcNormFactors’
plotDifftoBase: no visible global function definition for ‘is’
preAFold: no visible global function definition for ‘quantile’
preAFold: no visible global function definition for ‘var’
preAFold: no visible global function definition for ‘predict’
preAFoldComplex: no visible global function definition for ‘quantile’
preAFoldComplex: no visible global function definition for ‘var’
preAFoldComplex: no visible global function definition for ‘predict’
qtotalNormalized : rowQuar: no visible global function definition for
‘quantile’
qtotalNormalized : rowQuar: no visible global function definition for
‘sd’
qtotalNormalized : rowQuar: no visible global function definition for
‘median’
qtotalNormalized : rowQuar : <anonymous>: no visible global function
definition for ‘median’
replaceByrow: no visible global function definition for ‘median’
replaceByrow: no visible global function definition for ‘mad’
LevelstoNormFC<-,ABSDataSet-numeric: no visible global function
definition for ‘validObject’
[[<-,SumInfo-character-missing: no visible global function definition
for ‘as’
counts<-,ABSDataSet-matrix: no visible global function definition for
‘validObject’
excounts<-,ABSDataSet-matrix: no visible global function definition for
‘validObject’
groups<-,ABSDataSet-factor: no visible global function definition for
‘validObject’
maxRates<-,ABSDataSet-numeric: no visible global function definition
for ‘validObject’
minRates<-,ABSDataSet-numeric: no visible global function definition
for ‘validObject’
minimalDispersion<-,ABSDataSet-numeric: no visible global function
definition for ‘validObject’
normMethod<-,ABSDataSet-character: no visible global function
definition for ‘validObject’
paired<-,ABSDataSet-logical: no visible global function definition for
‘validObject’
sFactors<-,ABSDataSet-numeric: no visible global function definition
for ‘validObject’
Undefined global functions or variables:
as calcNormFactors is mad median model.matrix new p.adjust
p.adjust.methods pnbinom pnorm predict quantile sd validObject var
Consider adding
importFrom("methods", "as", "is", "new", "validObject")
importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
"p.adjust.methods", "pnbinom", "pnorm", "predict",
"quantile", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callParameter 9.977 0.270 14.223
plotDifftoBase 9.800 0.257 15.373
results 9.788 0.256 15.376
ABSSeq 9.642 0.368 15.176
callDEs 9.775 0.213 14.669
ReplaceOutliersByMAD 7.720 0.269 12.025
excounts 7.444 0.246 11.477
ABSSeqlm 6.493 0.198 10.148
genAFold 4.189 0.136 6.501
aFoldcomplexDesign 3.949 0.155 6.105
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ABSSeq.Rcheck/00check.log’
for details.
ABSSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ABSSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘ABSSeq’ ... ** using staged installation ** R ** data ** 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 (ABSSeq)
ABSSeq.Rcheck/ABSSeq-Ex.timings
| name | user | system | elapsed | |
| ABSDataSet | 0.019 | 0.001 | 0.030 | |
| ABSSeq | 9.642 | 0.368 | 15.176 | |
| ABSSeqlm | 6.493 | 0.198 | 10.148 | |
| LevelstoNormFC | 0.036 | 0.004 | 0.064 | |
| ReplaceOutliersByMAD | 7.720 | 0.269 | 12.025 | |
| aFoldcomplexDesign | 3.949 | 0.155 | 6.105 | |
| callDEs | 9.775 | 0.213 | 14.669 | |
| callParameter | 9.977 | 0.270 | 14.223 | |
| callParameterwithoutReplicates | 1.677 | 0.036 | 2.530 | |
| counts | 0.033 | 0.004 | 0.057 | |
| estimateSizeFactorsForMatrix | 0.050 | 0.004 | 0.073 | |
| excounts | 7.444 | 0.246 | 11.477 | |
| genAFold | 4.189 | 0.136 | 6.501 | |
| groups | 0.037 | 0.004 | 0.063 | |
| maxRates | 0.036 | 0.003 | 0.060 | |
| minRates | 0.035 | 0.003 | 0.058 | |
| minimalDispersion | 0.035 | 0.003 | 0.060 | |
| normMethod | 0.035 | 0.003 | 0.056 | |
| normalFactors | 2.517 | 0.094 | 3.996 | |
| paired | 0.035 | 0.004 | 0.058 | |
| plotDifftoBase | 9.800 | 0.257 | 15.373 | |
| qtotalNormalized | 2.690 | 0.102 | 4.311 | |
| results | 9.788 | 0.256 | 15.376 | |
| sFactors | 2.611 | 0.102 | 4.131 | |
| simuN5 | 0.030 | 0.003 | 0.051 | |