merida1 Summary
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| Package: octad |
| Version: 0.99.71 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data octad |
| BuildTime: 3 minutes 32.38 seconds |
| CheckCommand: BiocCheckGitClone('octad') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch octad_0.99.71.tar.gz && BiocCheck('octad_0.99.71.tar.gz', `new-package`=TRUE) |
| CheckTime: 13 minutes 52.17 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh octad_0.99.71.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 2.63 seconds |
| PackageFileSize: 244.05 KiB |
| BuildID:: octad_20220411185644 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: octad. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘octad/DESCRIPTION’ ... OK
* preparing ‘octad’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘octad_0.99.71.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('octad')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.71’
* package encoding: UTF-8
* checking package namespace information ... OK
OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'ExperimentHub'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad’ can be installed ... [57s/58s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘httr’
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 ... [56s/57s] NOTE
computeCellLine : pick.out.cell.line: no visible binding for global
variable ‘cell.line’
computeRefTissue: no visible binding for global variable ‘sample.type’
computeRefTissue: no visible binding for global variable ‘.’
computeRefTissue: no visible binding for global variable ‘sample.id’
diffExp: no visible global function definition for ‘pData’
diffExp: no visible binding for global variable ‘identifier’
diffExp: no visible binding for global variable ‘case’
diffExp: no visible binding for global variable ‘control’
octadDrugEnrichment: no visible global function definition for ‘mcols’
octadDrugEnrichment: no visible global function definition for ‘query’
runsRGES: no visible binding for global variable ‘cell_id’
runsRGES: no visible binding for global variable ‘pert_iname’
runsRGES: no visible binding for global variable ‘pert_id’
runsRGES: no visible binding for global variable ‘Symbol’
runsRGES: no visible binding for global variable ‘log2FoldChange’
runsRGES: no visible binding for global variable ‘pert_dose’
runsRGES: no visible binding for global variable ‘pert_time’
runsRGES: no visible binding for global variable ‘id.x’
runsRGES: no visible binding for global variable ‘id.y’
runsRGES: no visible binding for global variable ‘pert_time.x’
runsRGES: no visible binding for global variable ‘pert_dose.x’
runsRGES: no visible binding for global variable ‘RGES’
runsRGES: no visible binding for global variable ‘ouput’
topLineEval: no visible binding for global variable ‘sRGES’
topLineEval: no visible binding for global variable ‘medIC50’
topLineEval: no visible binding for global variable ‘pert_iname’
topLineEval: no visible binding for global variable ‘medauc’
Undefined global functions or variables:
. RGES Symbol case cell.line cell_id control id.x id.y identifier
log2FoldChange mcols medIC50 medauc ouput pData pert_dose pert_dose.x
pert_id pert_iname pert_time pert_time.x query sRGES sample.id
sample.type
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'computeCellLine.Rd':
\usage lines wider than 90 characters:
computeCellLine(case_id =case_id,expSet=NULL,LINCS_overlaps = TRUE, source='octad.small',file=NULL,output = FALSE,outputFolder='')
Rd file 'octadDrugEnrichment.Rd':
\usage lines wider than 90 characters:
octadDrugEnrichment(sRGES=NULL,target_type='chembl_targets',enrichFolder='enrichFolder',outputFolder=NULL)
Rd file 'runsRGES.Rd':
\examples lines wider than 100 characters:
sRGES=runsRGES(dz_signature=res_example,max_gene_size=100,permutations=1000,output=FALSE,outputFolder = tempdir())
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [361s/372s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runsRGES 171.671 4.069 177.001
topLineEval 46.500 0.788 48.450
computeCellLine 38.000 1.431 40.844
octadDrugEnrichment 35.829 3.475 37.097
diffExp 22.391 0.403 30.128
* 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: 5 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad.Rcheck/00check.log’
for details.
===============================
BiocCheck('octad_0.99.71.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
cmd: /Library/Frameworks/R.framework/Resources/bin/R
args: --vanilla -e 'library(octad)'
stderr:
Loading required package: magrittr
Loading required package: dplyr
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: ggplot2
Loading required package: edgeR
Error: package ‘limma’ required by ‘edgeR’ could not be found
Execution halted
* ERROR:
/Users/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad_0.99.71.tar.gz
must be loadable.
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad_0.99.71.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQ1jwSe/file130a9cd0028/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Epigenetics, Transcriptomics,
Coverage, Normalization, Pathways, Preprocessing, Bayesian,
Clustering, Regression, DNAMethylation, RNASeq, ChIPSeq,
CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialMethylation,
DifferentialSplicing, BatchEffect, MultipleComparison,
QualityControl, TimeCourse
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of octad...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/octadDrugEnrichment.R (line 94, column 19)
R/runsRGES_ultimate.R (line 63, column 19)
R/runsRGES_ultimate.R (line 66, column 19)
R/runsRGES_ultimate.R (line 80, column 21)
R/runsRGES_ultimate.R (line 83, column 21)
R/runsRGES_ultimate.R (line 193, column 8)
R/runsRGES_ultimate.R (line 229, column 16)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
computeCellLine.R (line 41, column 66)
computeCellLine.R (line 72, column 75)
computeRefTissue.R (line 45, column 57)
diffExp.R (line 40, column 66)
diffExp.R (line 44, column 68)
diffExp.R (line 85, column 50)
loadOctadCounts.R (line 17, column 63)
loadOctadCounts.R (line 24, column 61)
runsRGES_ultimate.R (line 192, column 98)
runsRGES_ultimate.R (line 193, column 122)
runsRGES_ultimate.R (line 231, column 23)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/octadDrugEnrichment.R (line 27, column 5)
cat() in R/octadDrugEnrichment.R (line 94, column 15)
print() in R/topLineEval.R (line 159, column 3)
print() in R/topLineEval.R (line 160, column 3)
print() in R/topLineEval.R (line 161, column 3)
print() in R/topLineEval.R (line 162, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/computeCellLine.R (line 6, column 17)
R/computeCellLine.R (line 14, column 18)
R/computeCellLine.R (line 19, column 22)
R/computeCellLine.R (line 20, column 17)
R/computeCellLine.R (line 21, column 17)
R/computeCellLine.R (line 22, column 24)
R/computeCellLine.R (line 23, column 51)
R/computeCellLine.R (line 24, column 26)
R/computeCellLine.R (line 26, column 20)
R/computeCellLine.R (line 27, column 17)
R/computeCellLine.R (line 29, column 11)
R/computeCellLine.R (line 30, column 17)
R/computeCellLine.R (line 32, column 24)
R/computeCellLine.R (line 33, column 13)
R/computeCellLine.R (line 38, column 17)
R/computeCellLine.R (line 39, column 13)
R/computeCellLine.R (line 40, column 17)
R/computeCellLine.R (line 41, column 27)
R/computeCellLine.R (line 42, column 27)
R/computeCellLine.R (line 43, column 13)
R/computeCellLine.R (line 45, column 17)
R/computeCellLine.R (line 49, column 24)
R/computeCellLine.R (line 50, column 17)
R/computeCellLine.R (line 55, column 17)
R/computeCellLine.R (line 59, column 19)
R/computeCellLine.R (line 60, column 17)
R/computeCellLine.R (line 62, column 33)
R/computeCellLine.R (line 63, column 17)
R/computeCellLine.R (line 65, column 23)
R/computeCellLine.R (line 66, column 31)
R/computeCellLine.R (line 67, column 7)
R/computeCellLine.R (line 68, column 12)
R/computeCellLine.R (line 69, column 13)
R/computeCellLine.R (line 70, column 11)
R/computeCellLine.R (line 71, column 33)
R/computeCellLine.R (line 72, column 52)
R/computeCellLine.R (line 73, column 25)
R/computeCellLine.R (line 75, column 35)
R/computeCellLine.R (line 76, column 20)
R/computeCellLine.R (line 81, column 11)
R/computeCellLine.R (line 87, column 13)
R/computeRefTissue.R (line 13, column 12)
R/computeRefTissue.R (line 14, column 13)
R/computeRefTissue.R (line 17, column 15)
R/computeRefTissue.R (line 18, column 20)
R/computeRefTissue.R (line 19, column 17)
R/computeRefTissue.R (line 20, column 17)
R/computeRefTissue.R (line 22, column 17)
R/computeRefTissue.R (line 27, column 15)
R/computeRefTissue.R (line 31, column 18)
R/computeRefTissue.R (line 34, column 13)
R/computeRefTissue.R (line 49, column 26)
R/computeRefTissue.R (line 52, column 12)
R/computeRefTissue.R (line 55, column 17)
R/computeRefTissue.R (line 56, column 12)
R/diffExp.R (line 7, column 9)
R/diffExp.R (line 17, column 18)
R/diffExp.R (line 20, column 14)
R/diffExp.R (line 21, column 7)
R/diffExp.R (line 22, column 11)
R/diffExp.R (line 24, column 16)
R/diffExp.R (line 37, column 17)
R/diffExp.R (line 38, column 13)
R/diffExp.R (line 39, column 17)
R/diffExp.R (line 40, column 27)
R/diffExp.R (line 41, column 27)
R/diffExp.R (line 42, column 13)
R/diffExp.R (line 43, column 19)
R/diffExp.R (line 44, column 29)
R/diffExp.R (line 45, column 29)
R/diffExp.R (line 46, column 16)
R/diffExp.R (line 49, column 12)
R/diffExp.R (line 55, column 24)
R/diffExp.R (line 56, column 12)
R/diffExp.R (line 61, column 20)
R/diffExp.R (line 62, column 20)
R/diffExp.R (line 63, column 10)
R/diffExp.R (line 64, column 10)
R/diffExp.R (line 65, column 27)
R/diffExp.R (line 66, column 32)
R/diffExp.R (line 68, column 16)
R/diffExp.R (line 69, column 10)
R/diffExp.R (line 70, column 7)
R/diffExp.R (line 75, column 12)
R/diffExp.R (line 76, column 7)
R/diffExp.R (line 77, column 7)
R/diffExp.R (line 78, column 7)
R/diffExp.R (line 79, column 7)
R/diffExp.R (line 80, column 9)
R/diffExp.R (line 81, column 9)
R/diffExp.R (line 83, column 9)
R/diffExp.R (line 84, column 7)
R/diffExp.R (line 85, column 15)
R/diffExp.R (line 90, column 10)
R/diffExp.R (line 96, column 33)
R/diffExp.R (line 97, column 13)
R/diffExp.R (line 99, column 11)
R/diffExp.R (line 101, column 11)
R/diffExp.R (line 105, column 11)
R/diffExp.R (line 107, column 11)
R/diffExp.R (line 110, column 10)
R/diffExp.R (line 111, column 12)
R/diffExp.R (line 112, column 9)
R/diffExp.R (line 113, column 20)
R/diffExp.R (line 114, column 9)
R/diffExp.R (line 121, column 16)
R/diffExp.R (line 123, column 16)
R/diffExp.R (line 125, column 16)
R/diffExp.R (line 127, column 14)
R/diffExp.R (line 130, column 14)
R/diffExp.R (line 131, column 14)
R/diffExp.R (line 133, column 12)
R/diffExp.R (line 134, column 12)
R/diffExp.R (line 135, column 12)
R/diffExp.R (line 136, column 9)
R/diffExp.R (line 138, column 9)
R/diffExp.R (line 140, column 9)
R/diffExp.R (line 141, column 19)
R/diffExp.R (line 142, column 14)
R/diffExp.R (line 143, column 20)
R/diffExp.R (line 144, column 9)
R/diffExp.R (line 149, column 7)
R/diffExp.R (line 150, column 14)
R/diffExp.R (line 151, column 10)
R/diffExp.R (line 152, column 11)
R/diffExp.R (line 153, column 12)
R/diffExp.R (line 154, column 22)
R/diffExp.R (line 155, column 18)
R/diffExp.R (line 157, column 7)
R/diffExp.R (line 158, column 10)
R/diffExp.R (line 159, column 10)
R/diffExp.R (line 160, column 10)
R/diffExp.R (line 162, column 10)
R/diffExp.R (line 163, column 8)
R/diffExp.R (line 166, column 19)
R/diffExp.R (line 167, column 19)
R/diffExp.R (line 169, column 9)
R/diffExp.R (line 170, column 19)
R/diffExp.R (line 171, column 20)
R/diffExp.R (line 174, column 22)
R/diffExp.R (line 175, column 30)
R/diffExp.R (line 176, column 25)
R/diffExp.R (line 177, column 29)
R/diffExp.R (line 178, column 27)
R/diffExp.R (line 179, column 9)
R/loadOctadCounts.R (line 13, column 15)
R/loadOctadCounts.R (line 14, column 11)
R/loadOctadCounts.R (line 17, column 14)
R/loadOctadCounts.R (line 18, column 24)
R/loadOctadCounts.R (line 19, column 24)
R/loadOctadCounts.R (line 24, column 14)
R/loadOctadCounts.R (line 25, column 24)
R/loadOctadCounts.R (line 26, column 24)
R/octadDrugEnrichment.R (line 6, column 21)
R/octadDrugEnrichment.R (line 17, column 18)
R/octadDrugEnrichment.R (line 24, column 16)
R/octadDrugEnrichment.R (line 25, column 21)
R/octadDrugEnrichment.R (line 28, column 20)
R/octadDrugEnrichment.R (line 34, column 15)
R/octadDrugEnrichment.R (line 35, column 14)
R/octadDrugEnrichment.R (line 36, column 21)
R/octadDrugEnrichment.R (line 41, column 15)
R/octadDrugEnrichment.R (line 43, column 11)
R/octadDrugEnrichment.R (line 50, column 23)
R/octadDrugEnrichment.R (line 51, column 13)
R/octadDrugEnrichment.R (line 52, column 20)
R/octadDrugEnrichment.R (line 53, column 20)
R/octadDrugEnrichment.R (line 54, column 20)
R/octadDrugEnrichment.R (line 60, column 32)
R/octadDrugEnrichment.R (line 61, column 32)
R/octadDrugEnrichment.R (line 62, column 22)
R/octadDrugEnrichment.R (line 64, column 16)
R/octadDrugEnrichment.R (line 68, column 16)
R/octadDrugEnrichment.R (line 69, column 16)
R/octadDrugEnrichment.R (line 71, column 21)
R/octadDrugEnrichment.R (line 73, column 23)
R/octadDrugEnrichment.R (line 76, column 23)
R/octadDrugEnrichment.R (line 80, column 24)
R/octadDrugEnrichment.R (line 81, column 24)
R/octadDrugEnrichment.R (line 82, column 32)
R/octadDrugEnrichment.R (line 91, column 26)
R/octadDrugEnrichment.R (line 93, column 30)
R/octadDrugEnrichment.R (line 95, column 25)
R/octadDrugEnrichment.R (line 96, column 33)
R/octadDrugEnrichment.R (line 97, column 30)
R/octadDrugEnrichment.R (line 98, column 38)
R/octadDrugEnrichment.R (line 102, column 14)
R/octadDrugEnrichment.R (line 105, column 16)
R/runsRGES_ultimate.R (line 19, column 18)
R/runsRGES_ultimate.R (line 23, column 14)
R/runsRGES_ultimate.R (line 31, column 18)
R/runsRGES_ultimate.R (line 48, column 23)
R/runsRGES_ultimate.R (line 53, column 20)
R/runsRGES_ultimate.R (line 54, column 18)
R/runsRGES_ultimate.R (line 55, column 20)
R/runsRGES_ultimate.R (line 56, column 22)
R/runsRGES_ultimate.R (line 57, column 24)
R/runsRGES_ultimate.R (line 113, column 28)
R/runsRGES_ultimate.R (line 114, column 20)
R/runsRGES_ultimate.R (line 118, column 11)
R/runsRGES_ultimate.R (line 121, column 20)
R/runsRGES_ultimate.R (line 124, column 15)
R/runsRGES_ultimate.R (line 147, column 15)
R/runsRGES_ultimate.R (line 149, column 17)
R/runsRGES_ultimate.R (line 172, column 5)
R/runsRGES_ultimate.R (line 173, column 15)
R/runsRGES_ultimate.R (line 175, column 22)
R/runsRGES_ultimate.R (line 176, column 16)
R/runsRGES_ultimate.R (line 177, column 20)
R/runsRGES_ultimate.R (line 178, column 18)
R/runsRGES_ultimate.R (line 183, column 20)
R/runsRGES_ultimate.R (line 187, column 22)
R/runsRGES_ultimate.R (line 190, column 22)
R/runsRGES_ultimate.R (line 224, column 10)
R/runsRGES_ultimate.R (line 252, column 6)
R/topLineEval.R (line 9, column 13)
R/topLineEval.R (line 18, column 18)
R/topLineEval.R (line 22, column 15)
R/topLineEval.R (line 23, column 20)
R/topLineEval.R (line 31, column 22)
R/topLineEval.R (line 33, column 15)
R/topLineEval.R (line 36, column 25)
R/topLineEval.R (line 37, column 25)
R/topLineEval.R (line 38, column 25)
R/topLineEval.R (line 40, column 15)
R/topLineEval.R (line 41, column 13)
R/topLineEval.R (line 44, column 15)
R/topLineEval.R (line 45, column 24)
R/topLineEval.R (line 46, column 32)
R/topLineEval.R (line 47, column 30)
R/topLineEval.R (line 48, column 31)
R/topLineEval.R (line 49, column 32)
R/topLineEval.R (line 51, column 24)
R/topLineEval.R (line 54, column 14)
R/topLineEval.R (line 57, column 24)
R/topLineEval.R (line 58, column 24)
R/topLineEval.R (line 59, column 24)
R/topLineEval.R (line 61, column 14)
R/topLineEval.R (line 62, column 12)
R/topLineEval.R (line 66, column 14)
R/topLineEval.R (line 67, column 22)
R/topLineEval.R (line 68, column 29)
R/topLineEval.R (line 69, column 28)
R/topLineEval.R (line 70, column 29)
R/topLineEval.R (line 71, column 30)
R/topLineEval.R (line 73, column 22)
R/topLineEval.R (line 74, column 22)
R/topLineEval.R (line 75, column 31)
R/topLineEval.R (line 76, column 10)
R/topLineEval.R (line 77, column 16)
R/topLineEval.R (line 78, column 12)
R/topLineEval.R (line 79, column 11)
R/topLineEval.R (line 80, column 11)
R/topLineEval.R (line 82, column 28)
R/topLineEval.R (line 83, column 28)
R/topLineEval.R (line 85, column 21)
R/topLineEval.R (line 87, column 16)
R/topLineEval.R (line 88, column 17)
R/topLineEval.R (line 89, column 17)
R/topLineEval.R (line 90, column 9)
R/topLineEval.R (line 91, column 9)
R/topLineEval.R (line 92, column 9)
R/topLineEval.R (line 94, column 5)
R/topLineEval.R (line 100, column 6)
R/topLineEval.R (line 103, column 13)
R/topLineEval.R (line 110, column 13)
R/topLineEval.R (line 117, column 11)
R/topLineEval.R (line 118, column 15)
R/topLineEval.R (line 120, column 29)
R/topLineEval.R (line 121, column 29)
R/topLineEval.R (line 122, column 21)
R/topLineEval.R (line 123, column 11)
R/topLineEval.R (line 124, column 10)
R/topLineEval.R (line 126, column 16)
R/topLineEval.R (line 127, column 17)
R/topLineEval.R (line 128, column 17)
R/topLineEval.R (line 129, column 9)
R/topLineEval.R (line 130, column 9)
R/topLineEval.R (line 131, column 9)
R/topLineEval.R (line 134, column 5)
R/topLineEval.R (line 139, column 6)
R/topLineEval.R (line 142, column 12)
R/topLineEval.R (line 147, column 13)
R/topLineEval.R (line 155, column 7)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
<<- in R/zzz.R (line 5, column 7)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17
times)
suppressMessages() in R/computeCellLine.R (line 49, column 26)
suppressMessages() in R/computeCellLine.R (line 59, column 21)
suppressMessages() in R/computeCellLine.R (line 62, column 35)
suppressMessages() in R/computeCellLine.R (line 66, column 33)
suppressMessages() in R/computeRefTissue.R (line 13, column 14)
suppressMessages() in R/computeRefTissue.R (line 17, column 17)
suppressMessages() in R/diffExp.R (line 55, column 26)
suppressMessages() in R/diffExp.R (line 174, column 24)
suppressMessages() in R/octadDrugEnrichment.R (line 24, column
18)
suppressMessages() in R/octadDrugEnrichment.R (line 25, column
23)
suppressMessages() in R/octadDrugEnrichment.R (line 34, column
17)
suppressMessages() in R/runsRGES_ultimate.R (line 31, column
20)
suppressMessages() in R/runsRGES_ultimate.R (line 121, column
22)
suppressMessages() in R/runsRGES_ultimate.R (line 124, column
17)
suppressMessages() in R/runsRGES_ultimate.R (line 183, column
22)
suppressMessages() in R/topLineEval.R (line 33, column 46)
suppressMessages() in R/topLineEval.R (line 54, column 45)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
runsRGES() (R/runsRGES_ultimate.R, line 8): 248 lines
diffExp() (R/diffExp.R, line 7): 176 lines
topLineEval() (R/topLineEval.R, line 9): 159 lines
octadDrugEnrichment() (R/octadDrugEnrichment.R, line 6): 107
lines
computeRefTissue() (R/computeRefTissue.R, line 6): 87 lines
* Checking man page documentation...
snapshotDate(): 2022-04-06
snapshotDate(): 2022-04-06
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 272 lines (18%) are > 80 characters
long.
First 6 lines:
R/computeCellLine.R:7 computeCellLine = function(case_id = case_id, exp...
R/computeCellLine.R:20 pick.out.cell.line = function(expr.of.samples,...
R/computeCellLine.R:23 correlation.matrix = cor(expr.of.samples[mar...
R/computeCellLine.R:28 p.value.vec = foreach::foreach(cell.line = s...
R/computeCellLine.R:31 p.value = wilcox.test(correlation.matrix...
R/computeCellLine.R:35 list(cell.line.median.cor = cell.line.median...
* NOTE: Consider multiples of 4 spaces for line indents, 584
lines(39%) are not.
First 6 lines:
R/computeCellLine.R:8 outputFolder = NULL) {
R/computeCellLine.R:9 # STOPS
R/computeCellLine.R:10 if (missing(case_id)) {
R/computeCellLine.R:12 }
R/computeCellLine.R:13
R/computeCellLine.R:14 if (is.null(outputFolder)) {
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir octad_0.99.71.tar.gz'
>>>>>>>
* installing *source* package ‘octad’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2022-04-06
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-04-06
snapshotDate(): 2022-04-06
** testing if installed package can be loaded from final location
snapshotDate(): 2022-04-06
snapshotDate(): 2022-04-06
** testing if installed package keeps a record of temporary installation path
* DONE (octad)
nebbiolo1 Summary
[top]
| Package: octad |
| Version: 0.99.71 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data octad |
| BuildTime: 2 minutes 18.30 seconds |
| CheckCommand: BiocCheckGitClone('octad') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings octad_0.99.71.tar.gz && BiocCheck('octad_0.99.71.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 1.09 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 244.16 KiB |
| BuildID:: octad_20220411185644 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: octad. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘octad/DESCRIPTION’ ... OK
* preparing ‘octad’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘octad_0.99.71.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('octad')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.71’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'ExperimentHub'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad’ can be installed ... [37s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘httr’
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 ... [40s/41s] NOTE
computeCellLine : pick.out.cell.line: no visible binding for global
variable ‘cell.line’
computeRefTissue: no visible binding for global variable ‘sample.type’
computeRefTissue: no visible binding for global variable ‘.’
computeRefTissue: no visible binding for global variable ‘sample.id’
diffExp: no visible global function definition for ‘pData’
diffExp: no visible binding for global variable ‘identifier’
diffExp: no visible binding for global variable ‘case’
diffExp: no visible binding for global variable ‘control’
octadDrugEnrichment: no visible global function definition for ‘mcols’
octadDrugEnrichment: no visible global function definition for ‘query’
runsRGES: no visible binding for global variable ‘cell_id’
runsRGES: no visible binding for global variable ‘pert_iname’
runsRGES: no visible binding for global variable ‘pert_id’
runsRGES: no visible binding for global variable ‘Symbol’
runsRGES: no visible binding for global variable ‘log2FoldChange’
runsRGES: no visible binding for global variable ‘pert_dose’
runsRGES: no visible binding for global variable ‘pert_time’
runsRGES: no visible binding for global variable ‘id.x’
runsRGES: no visible binding for global variable ‘id.y’
runsRGES: no visible binding for global variable ‘pert_time.x’
runsRGES: no visible binding for global variable ‘pert_dose.x’
runsRGES: no visible binding for global variable ‘RGES’
runsRGES: no visible binding for global variable ‘ouput’
topLineEval: no visible binding for global variable ‘sRGES’
topLineEval: no visible binding for global variable ‘medIC50’
topLineEval: no visible binding for global variable ‘pert_iname’
topLineEval: no visible binding for global variable ‘medauc’
Undefined global functions or variables:
. RGES Symbol case cell.line cell_id control id.x id.y identifier
log2FoldChange mcols medIC50 medauc ouput pData pert_dose pert_dose.x
pert_id pert_iname pert_time pert_time.x query sRGES sample.id
sample.type
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'computeCellLine.Rd':
\usage lines wider than 90 characters:
computeCellLine(case_id =case_id,expSet=NULL,LINCS_overlaps = TRUE, source='octad.small',file=NULL,output = FALSE,outputFolder='')
Rd file 'octadDrugEnrichment.Rd':
\usage lines wider than 90 characters:
octadDrugEnrichment(sRGES=NULL,target_type='chembl_targets',enrichFolder='enrichFolder',outputFolder=NULL)
Rd file 'runsRGES.Rd':
\examples lines wider than 100 characters:
sRGES=runsRGES(dz_signature=res_example,max_gene_size=100,permutations=1000,output=FALSE,outputFolder = tempdir())
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [239s/241s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runsRGES 111.175 3.077 115.158
computeCellLine 29.051 1.512 32.357
octadDrugEnrichment 27.969 2.592 29.426
topLineEval 23.509 0.939 21.695
diffExp 14.685 0.449 16.449
* 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: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad.Rcheck/00check.log’
for details.
===============================
BiocCheck('octad_0.99.71.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2391/09c049d20f86eb269e438e0c55d124f6c7ff0187/octad_0.99.71.tar.gz" "/tmp/RtmpNQSLRB/filef5ff6a477ea0/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Epigenetics, Transcriptomics,
Coverage, Normalization, Pathways, Preprocessing, Bayesian,
Clustering, Regression, DNAMethylation, RNASeq, ChIPSeq,
CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialMethylation,
DifferentialSplicing, BatchEffect, MultipleComparison,
QualityControl, TimeCourse
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of octad...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/octadDrugEnrichment.R (line 94, column 19)
R/runsRGES_ultimate.R (line 63, column 19)
R/runsRGES_ultimate.R (line 66, column 19)
R/runsRGES_ultimate.R (line 80, column 21)
R/runsRGES_ultimate.R (line 83, column 21)
R/runsRGES_ultimate.R (line 193, column 8)
R/runsRGES_ultimate.R (line 229, column 16)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
computeCellLine.R (line 41, column 66)
computeCellLine.R (line 72, column 75)
computeRefTissue.R (line 45, column 57)
diffExp.R (line 40, column 66)
diffExp.R (line 44, column 68)
diffExp.R (line 85, column 50)
loadOctadCounts.R (line 17, column 63)
loadOctadCounts.R (line 24, column 61)
runsRGES_ultimate.R (line 192, column 98)
runsRGES_ultimate.R (line 193, column 122)
runsRGES_ultimate.R (line 231, column 23)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/octadDrugEnrichment.R (line 27, column 5)
cat() in R/octadDrugEnrichment.R (line 94, column 15)
print() in R/topLineEval.R (line 159, column 3)
print() in R/topLineEval.R (line 160, column 3)
print() in R/topLineEval.R (line 161, column 3)
print() in R/topLineEval.R (line 162, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/computeCellLine.R (line 6, column 17)
R/computeCellLine.R (line 14, column 18)
R/computeCellLine.R (line 19, column 22)
R/computeCellLine.R (line 20, column 17)
R/computeCellLine.R (line 21, column 17)
R/computeCellLine.R (line 22, column 24)
R/computeCellLine.R (line 23, column 51)
R/computeCellLine.R (line 24, column 26)
R/computeCellLine.R (line 26, column 20)
R/computeCellLine.R (line 27, column 17)
R/computeCellLine.R (line 29, column 11)
R/computeCellLine.R (line 30, column 17)
R/computeCellLine.R (line 32, column 24)
R/computeCellLine.R (line 33, column 13)
R/computeCellLine.R (line 38, column 17)
R/computeCellLine.R (line 39, column 13)
R/computeCellLine.R (line 40, column 17)
R/computeCellLine.R (line 41, column 27)
R/computeCellLine.R (line 42, column 27)
R/computeCellLine.R (line 43, column 13)
R/computeCellLine.R (line 45, column 17)
R/computeCellLine.R (line 49, column 24)
R/computeCellLine.R (line 50, column 17)
R/computeCellLine.R (line 55, column 17)
R/computeCellLine.R (line 59, column 19)
R/computeCellLine.R (line 60, column 17)
R/computeCellLine.R (line 62, column 33)
R/computeCellLine.R (line 63, column 17)
R/computeCellLine.R (line 65, column 23)
R/computeCellLine.R (line 66, column 31)
R/computeCellLine.R (line 67, column 7)
R/computeCellLine.R (line 68, column 12)
R/computeCellLine.R (line 69, column 13)
R/computeCellLine.R (line 70, column 11)
R/computeCellLine.R (line 71, column 33)
R/computeCellLine.R (line 72, column 52)
R/computeCellLine.R (line 73, column 25)
R/computeCellLine.R (line 75, column 35)
R/computeCellLine.R (line 76, column 20)
R/computeCellLine.R (line 81, column 11)
R/computeCellLine.R (line 87, column 13)
R/computeRefTissue.R (line 13, column 12)
R/computeRefTissue.R (line 14, column 13)
R/computeRefTissue.R (line 17, column 15)
R/computeRefTissue.R (line 18, column 20)
R/computeRefTissue.R (line 19, column 17)
R/computeRefTissue.R (line 20, column 17)
R/computeRefTissue.R (line 22, column 17)
R/computeRefTissue.R (line 27, column 15)
R/computeRefTissue.R (line 31, column 18)
R/computeRefTissue.R (line 34, column 13)
R/computeRefTissue.R (line 49, column 26)
R/computeRefTissue.R (line 52, column 12)
R/computeRefTissue.R (line 55, column 17)
R/computeRefTissue.R (line 56, column 12)
R/diffExp.R (line 7, column 9)
R/diffExp.R (line 17, column 18)
R/diffExp.R (line 20, column 14)
R/diffExp.R (line 21, column 7)
R/diffExp.R (line 22, column 11)
R/diffExp.R (line 24, column 16)
R/diffExp.R (line 37, column 17)
R/diffExp.R (line 38, column 13)
R/diffExp.R (line 39, column 17)
R/diffExp.R (line 40, column 27)
R/diffExp.R (line 41, column 27)
R/diffExp.R (line 42, column 13)
R/diffExp.R (line 43, column 19)
R/diffExp.R (line 44, column 29)
R/diffExp.R (line 45, column 29)
R/diffExp.R (line 46, column 16)
R/diffExp.R (line 49, column 12)
R/diffExp.R (line 55, column 24)
R/diffExp.R (line 56, column 12)
R/diffExp.R (line 61, column 20)
R/diffExp.R (line 62, column 20)
R/diffExp.R (line 63, column 10)
R/diffExp.R (line 64, column 10)
R/diffExp.R (line 65, column 27)
R/diffExp.R (line 66, column 32)
R/diffExp.R (line 68, column 16)
R/diffExp.R (line 69, column 10)
R/diffExp.R (line 70, column 7)
R/diffExp.R (line 75, column 12)
R/diffExp.R (line 76, column 7)
R/diffExp.R (line 77, column 7)
R/diffExp.R (line 78, column 7)
R/diffExp.R (line 79, column 7)
R/diffExp.R (line 80, column 9)
R/diffExp.R (line 81, column 9)
R/diffExp.R (line 83, column 9)
R/diffExp.R (line 84, column 7)
R/diffExp.R (line 85, column 15)
R/diffExp.R (line 90, column 10)
R/diffExp.R (line 96, column 33)
R/diffExp.R (line 97, column 13)
R/diffExp.R (line 99, column 11)
R/diffExp.R (line 101, column 11)
R/diffExp.R (line 105, column 11)
R/diffExp.R (line 107, column 11)
R/diffExp.R (line 110, column 10)
R/diffExp.R (line 111, column 12)
R/diffExp.R (line 112, column 9)
R/diffExp.R (line 113, column 20)
R/diffExp.R (line 114, column 9)
R/diffExp.R (line 121, column 16)
R/diffExp.R (line 123, column 16)
R/diffExp.R (line 125, column 16)
R/diffExp.R (line 127, column 14)
R/diffExp.R (line 130, column 14)
R/diffExp.R (line 131, column 14)
R/diffExp.R (line 133, column 12)
R/diffExp.R (line 134, column 12)
R/diffExp.R (line 135, column 12)
R/diffExp.R (line 136, column 9)
R/diffExp.R (line 138, column 9)
R/diffExp.R (line 140, column 9)
R/diffExp.R (line 141, column 19)
R/diffExp.R (line 142, column 14)
R/diffExp.R (line 143, column 20)
R/diffExp.R (line 144, column 9)
R/diffExp.R (line 149, column 7)
R/diffExp.R (line 150, column 14)
R/diffExp.R (line 151, column 10)
R/diffExp.R (line 152, column 11)
R/diffExp.R (line 153, column 12)
R/diffExp.R (line 154, column 22)
R/diffExp.R (line 155, column 18)
R/diffExp.R (line 157, column 7)
R/diffExp.R (line 158, column 10)
R/diffExp.R (line 159, column 10)
R/diffExp.R (line 160, column 10)
R/diffExp.R (line 162, column 10)
R/diffExp.R (line 163, column 8)
R/diffExp.R (line 166, column 19)
R/diffExp.R (line 167, column 19)
R/diffExp.R (line 169, column 9)
R/diffExp.R (line 170, column 19)
R/diffExp.R (line 171, column 20)
R/diffExp.R (line 174, column 22)
R/diffExp.R (line 175, column 30)
R/diffExp.R (line 176, column 25)
R/diffExp.R (line 177, column 29)
R/diffExp.R (line 178, column 27)
R/diffExp.R (line 179, column 9)
R/loadOctadCounts.R (line 13, column 15)
R/loadOctadCounts.R (line 14, column 11)
R/loadOctadCounts.R (line 17, column 14)
R/loadOctadCounts.R (line 18, column 24)
R/loadOctadCounts.R (line 19, column 24)
R/loadOctadCounts.R (line 24, column 14)
R/loadOctadCounts.R (line 25, column 24)
R/loadOctadCounts.R (line 26, column 24)
R/octadDrugEnrichment.R (line 6, column 21)
R/octadDrugEnrichment.R (line 17, column 18)
R/octadDrugEnrichment.R (line 24, column 16)
R/octadDrugEnrichment.R (line 25, column 21)
R/octadDrugEnrichment.R (line 28, column 20)
R/octadDrugEnrichment.R (line 34, column 15)
R/octadDrugEnrichment.R (line 35, column 14)
R/octadDrugEnrichment.R (line 36, column 21)
R/octadDrugEnrichment.R (line 41, column 15)
R/octadDrugEnrichment.R (line 43, column 11)
R/octadDrugEnrichment.R (line 50, column 23)
R/octadDrugEnrichment.R (line 51, column 13)
R/octadDrugEnrichment.R (line 52, column 20)
R/octadDrugEnrichment.R (line 53, column 20)
R/octadDrugEnrichment.R (line 54, column 20)
R/octadDrugEnrichment.R (line 60, column 32)
R/octadDrugEnrichment.R (line 61, column 32)
R/octadDrugEnrichment.R (line 62, column 22)
R/octadDrugEnrichment.R (line 64, column 16)
R/octadDrugEnrichment.R (line 68, column 16)
R/octadDrugEnrichment.R (line 69, column 16)
R/octadDrugEnrichment.R (line 71, column 21)
R/octadDrugEnrichment.R (line 73, column 23)
R/octadDrugEnrichment.R (line 76, column 23)
R/octadDrugEnrichment.R (line 80, column 24)
R/octadDrugEnrichment.R (line 81, column 24)
R/octadDrugEnrichment.R (line 82, column 32)
R/octadDrugEnrichment.R (line 91, column 26)
R/octadDrugEnrichment.R (line 93, column 30)
R/octadDrugEnrichment.R (line 95, column 25)
R/octadDrugEnrichment.R (line 96, column 33)
R/octadDrugEnrichment.R (line 97, column 30)
R/octadDrugEnrichment.R (line 98, column 38)
R/octadDrugEnrichment.R (line 102, column 14)
R/octadDrugEnrichment.R (line 105, column 16)
R/runsRGES_ultimate.R (line 19, column 18)
R/runsRGES_ultimate.R (line 23, column 14)
R/runsRGES_ultimate.R (line 31, column 18)
R/runsRGES_ultimate.R (line 48, column 23)
R/runsRGES_ultimate.R (line 53, column 20)
R/runsRGES_ultimate.R (line 54, column 18)
R/runsRGES_ultimate.R (line 55, column 20)
R/runsRGES_ultimate.R (line 56, column 22)
R/runsRGES_ultimate.R (line 57, column 24)
R/runsRGES_ultimate.R (line 113, column 28)
R/runsRGES_ultimate.R (line 114, column 20)
R/runsRGES_ultimate.R (line 118, column 11)
R/runsRGES_ultimate.R (line 121, column 20)
R/runsRGES_ultimate.R (line 124, column 15)
R/runsRGES_ultimate.R (line 147, column 15)
R/runsRGES_ultimate.R (line 149, column 17)
R/runsRGES_ultimate.R (line 172, column 5)
R/runsRGES_ultimate.R (line 173, column 15)
R/runsRGES_ultimate.R (line 175, column 22)
R/runsRGES_ultimate.R (line 176, column 16)
R/runsRGES_ultimate.R (line 177, column 20)
R/runsRGES_ultimate.R (line 178, column 18)
R/runsRGES_ultimate.R (line 183, column 20)
R/runsRGES_ultimate.R (line 187, column 22)
R/runsRGES_ultimate.R (line 190, column 22)
R/runsRGES_ultimate.R (line 224, column 10)
R/runsRGES_ultimate.R (line 252, column 6)
R/topLineEval.R (line 9, column 13)
R/topLineEval.R (line 18, column 18)
R/topLineEval.R (line 22, column 15)
R/topLineEval.R (line 23, column 20)
R/topLineEval.R (line 31, column 22)
R/topLineEval.R (line 33, column 15)
R/topLineEval.R (line 36, column 25)
R/topLineEval.R (line 37, column 25)
R/topLineEval.R (line 38, column 25)
R/topLineEval.R (line 40, column 15)
R/topLineEval.R (line 41, column 13)
R/topLineEval.R (line 44, column 15)
R/topLineEval.R (line 45, column 24)
R/topLineEval.R (line 46, column 32)
R/topLineEval.R (line 47, column 30)
R/topLineEval.R (line 48, column 31)
R/topLineEval.R (line 49, column 32)
R/topLineEval.R (line 51, column 24)
R/topLineEval.R (line 54, column 14)
R/topLineEval.R (line 57, column 24)
R/topLineEval.R (line 58, column 24)
R/topLineEval.R (line 59, column 24)
R/topLineEval.R (line 61, column 14)
R/topLineEval.R (line 62, column 12)
R/topLineEval.R (line 66, column 14)
R/topLineEval.R (line 67, column 22)
R/topLineEval.R (line 68, column 29)
R/topLineEval.R (line 69, column 28)
R/topLineEval.R (line 70, column 29)
R/topLineEval.R (line 71, column 30)
R/topLineEval.R (line 73, column 22)
R/topLineEval.R (line 74, column 22)
R/topLineEval.R (line 75, column 31)
R/topLineEval.R (line 76, column 10)
R/topLineEval.R (line 77, column 16)
R/topLineEval.R (line 78, column 12)
R/topLineEval.R (line 79, column 11)
R/topLineEval.R (line 80, column 11)
R/topLineEval.R (line 82, column 28)
R/topLineEval.R (line 83, column 28)
R/topLineEval.R (line 85, column 21)
R/topLineEval.R (line 87, column 16)
R/topLineEval.R (line 88, column 17)
R/topLineEval.R (line 89, column 17)
R/topLineEval.R (line 90, column 9)
R/topLineEval.R (line 91, column 9)
R/topLineEval.R (line 92, column 9)
R/topLineEval.R (line 94, column 5)
R/topLineEval.R (line 100, column 6)
R/topLineEval.R (line 103, column 13)
R/topLineEval.R (line 110, column 13)
R/topLineEval.R (line 117, column 11)
R/topLineEval.R (line 118, column 15)
R/topLineEval.R (line 120, column 29)
R/topLineEval.R (line 121, column 29)
R/topLineEval.R (line 122, column 21)
R/topLineEval.R (line 123, column 11)
R/topLineEval.R (line 124, column 10)
R/topLineEval.R (line 126, column 16)
R/topLineEval.R (line 127, column 17)
R/topLineEval.R (line 128, column 17)
R/topLineEval.R (line 129, column 9)
R/topLineEval.R (line 130, column 9)
R/topLineEval.R (line 131, column 9)
R/topLineEval.R (line 134, column 5)
R/topLineEval.R (line 139, column 6)
R/topLineEval.R (line 142, column 12)
R/topLineEval.R (line 147, column 13)
R/topLineEval.R (line 155, column 7)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
<<- in R/zzz.R (line 5, column 7)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17
times)
suppressMessages() in R/computeCellLine.R (line 49, column 26)
suppressMessages() in R/computeCellLine.R (line 59, column 21)
suppressMessages() in R/computeCellLine.R (line 62, column 35)
suppressMessages() in R/computeCellLine.R (line 66, column 33)
suppressMessages() in R/computeRefTissue.R (line 13, column 14)
suppressMessages() in R/computeRefTissue.R (line 17, column 17)
suppressMessages() in R/diffExp.R (line 55, column 26)
suppressMessages() in R/diffExp.R (line 174, column 24)
suppressMessages() in R/octadDrugEnrichment.R (line 24, column
18)
suppressMessages() in R/octadDrugEnrichment.R (line 25, column
23)
suppressMessages() in R/octadDrugEnrichment.R (line 34, column
17)
suppressMessages() in R/runsRGES_ultimate.R (line 31, column
20)
suppressMessages() in R/runsRGES_ultimate.R (line 121, column
22)
suppressMessages() in R/runsRGES_ultimate.R (line 124, column
17)
suppressMessages() in R/runsRGES_ultimate.R (line 183, column
22)
suppressMessages() in R/topLineEval.R (line 33, column 46)
suppressMessages() in R/topLineEval.R (line 54, column 45)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
runsRGES() (R/runsRGES_ultimate.R, line 8): 248 lines
diffExp() (R/diffExp.R, line 7): 176 lines
topLineEval() (R/topLineEval.R, line 9): 159 lines
octadDrugEnrichment() (R/octadDrugEnrichment.R, line 6): 107
lines
computeRefTissue() (R/computeRefTissue.R, line 6): 87 lines
* Checking man page documentation...
snapshotDate(): 2022-04-06
snapshotDate(): 2022-04-06
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 272 lines (18%) are > 80 characters
long.
First 6 lines:
R/computeCellLine.R:7 computeCellLine = function(case_id = case_id, exp...
R/computeCellLine.R:20 pick.out.cell.line = function(expr.of.samples,...
R/computeCellLine.R:23 correlation.matrix = cor(expr.of.samples[mar...
R/computeCellLine.R:28 p.value.vec = foreach::foreach(cell.line = s...
R/computeCellLine.R:31 p.value = wilcox.test(correlation.matrix...
R/computeCellLine.R:35 list(cell.line.median.cor = cell.line.median...
* NOTE: Consider multiples of 4 spaces for line indents, 584
lines(39%) are not.
First 6 lines:
R/computeCellLine.R:8 outputFolder = NULL) {
R/computeCellLine.R:9 # STOPS
R/computeCellLine.R:10 if (missing(case_id)) {
R/computeCellLine.R:12 }
R/computeCellLine.R:13
R/computeCellLine.R:14 if (is.null(outputFolder)) {
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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