===============================
BiocCheckGitClone('octad')
===============================
This is BiocCheckGitClone version 1.30.0. 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...
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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/7360f8d93836602b3e6ccba5b88f60629e5fd03c/octad.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘0.99.29’
* 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', 'doParallel', '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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad’ can be installed ... [31s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘ExperimentHub’
A package should be listed in only one of these fields.
* 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: ‘doParallel’
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 ... [32s/32s] NOTE
computeCellLine : pick.out.cell.line: no visible binding for global
variable ‘cell.line’
computeCellLine: no visible global function definition for ‘write.csv’
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’
computeRefTissue: no visible global function definition for ‘write.csv’
diffExp: no visible global function definition for ‘pData’
diffExp: no visible global function definition for ‘write.csv’
diffExp: no visible binding for global variable ‘identifier’
diffExp: no visible binding for global variable ‘case’
diffExp: no visible binding for global variable ‘control’
geneEnrich: no visible global function definition for ‘write.csv’
octadDrugEnrichment: no visible global function definition for ‘mcols’
octadDrugEnrichment: no visible global function definition for ‘query’
octadDrugEnrichment: no visible binding for global variable ‘title’
octadDrugEnrichment: no visible global function definition for
‘write.csv’
octadDrugEnrichment: no visible global function definition for ‘pdf’
octadDrugEnrichment: no visible global function definition for
‘dev.off’
octadDrugEnrichment: no visible global function definition for
‘read.csv2’
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 global function definition for ‘write.csv’
runsRGES: no visible binding for global variable ‘Symbol’
runsRGES: no visible binding for global variable ‘log2FoldChange’
runsRGES: no visible global function definition for ‘head’
runsRGES: no visible global function definition for ‘txtProgressBar’
runsRGES: no visible global function definition for ‘read.csv’
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’
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 dev.off head id.x id.y
identifier log2FoldChange mcols medIC50 medauc pData pdf pert_dose
pert_dose.x pert_id pert_iname pert_time pert_time.x query read.csv
read.csv2 sRGES sample.id sample.type title txtProgressBar write.csv
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "title")
importFrom("utils", "head", "read.csv", "read.csv2", "txtProgressBar",
"write.csv")
to your NAMESPACE file.
* 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,returnDF = FALSE)
\examples lines wider than 100 characters:
HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'primary') #select data
Rd file 'computeRefTissue.Rd':
\usage lines wider than 90 characters:
computeRefTissue(case_id=NULL,adjacent=FALSE,source='octad',n_varGenes = 500,method='varGenes',expSet=NULL,control_size = length(case_ ... [TRUNCATED]
\examples lines wider than 100 characters:
control_id=computeRefTissue(case_id,outputFolder='',output=TRUE, expSet = "octad",control_size = 50)
Rd file 'diffExp.Rd':
\examples lines wider than 100 characters:
HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'primary') #select data
HCC_adjacent=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'adjacent'&data.source == 'TCGA') #select data
Rd file 'loadOctadCounts.Rd':
\examples lines wider than 100 characters:
#HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'primary') #select data
Rd file 'octadDrugEnrichment.Rd':
\examples lines wider than 100 characters:
#load example sRGES computed by runsRGES() function for HCC vs liver adjacent tissues on octad.small dataset
Rd file 'runsRGES.Rd':
\usage lines wider than 90 characters:
cells=NULL,outputFolder=NULL,weight_cell_line=NULL,permutations=10000)
\examples lines wider than 100 characters:
#load differential expression example for HCC vs adjacent liver tissue computed in diffExp() function
Rd file 'topLineEval.Rd':
\examples lines wider than 100 characters:
#load example sRGES computed by runsRGES() function for HCC vs liver adjacent tissues on octad.small dataset
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 ... [224s/236s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runsRGES 102.280 5.114 108.657
computeCellLine 36.031 1.572 40.683
octadDrugEnrichment 31.331 0.759 33.721
diffExp 18.475 0.436 20.639
computeRefTissue 5.106 0.308 6.975
* 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/2391/7360f8d93836602b3e6ccba5b88f60629e5fd03c/octad.Rcheck/00check.log’
for details.
===============================
BiocCheck('octad_0.99.29.tar.gz')
===============================
This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 39 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
computeCellLine (cell.line)
computeCellLine (write.csv)
computeRefTissue (sample.type)
computeRefTissue (.)
computeRefTissue (sample.id)
computeRefTissue (write.csv)
diffExp (pData)
diffExp (write.csv)
diffExp (identifier)
diffExp (case)
diffExp (control)
geneEnrich (write.csv)
octadDrugEnrichment (mcols)
octadDrugEnrichment (query)
octadDrugEnrichment (title)
octadDrugEnrichment (write.csv)
octadDrugEnrichment (pdf)
octadDrugEnrichment (dev.off)
octadDrugEnrichment (read.csv2)
runsRGES (cell_id)
runsRGES (pert_iname)
runsRGES (pert_id)
runsRGES (write.csv)
runsRGES (Symbol)
runsRGES (log2FoldChange)
runsRGES (head)
runsRGES (txtProgressBar)
runsRGES (read.csv)
runsRGES (pert_dose)
runsRGES (pert_time)
runsRGES (id.x)
runsRGES (id.y)
runsRGES (pert_time.x)
runsRGES (pert_dose.x)
runsRGES (RGES)
topLineEval (sRGES)
topLineEval (medIC50)
topLineEval (pert_iname)
topLineEval (medauc)
* 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...
* 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, ThirdPartyClient, DataImport, GUI
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 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 87, column 13)
R/runsRGES_ultimate.R (line 51, column 29)
R/runsRGES_ultimate.R (line 54, column 29)
R/runsRGES_ultimate.R (line 70, column 31)
R/runsRGES_ultimate.R (line 73, column 31)
R/runsRGES_ultimate.R (line 260, column 14)
R/runsRGES_ultimate.R (line 298, column 22)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
computeCellLine.R (line 42, column 60)
computeCellLine.R (line 95, column 76)
computeRefTissue.R (line 75, column 58)
diffExp.R (line 39, column 60)
diffExp.R (line 43, column 62)
diffExp.R (line 117, column 54)
geneEnrich.R (line 28, column 19)
loadOctadCounts.R (line 14, column 65)
loadOctadCounts.R (line 24, column 63)
runsRGES_ultimate.R (line 256, column 61)
runsRGES_ultimate.R (line 257, column 61)
runsRGES_ultimate.R (line 298, column 29)
* Checking parsed R code in R directory, examples, vignettes...
* 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 10): 315 lines
diffExp() (R/diffExp.R, line 8): 232 lines
topLineEval() (R/topLineEval.R, line 10): 171 lines
computeRefTissue() (R/computeRefTissue.R, line 7): 121 lines
computeCellLine() (R/computeCellLine.R, line 7): 119 lines
* Checking man page documentation...
* 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; 295 lines (17%) are > 80 characters
long.
First 6 lines:
R/computeCellLine.R:7 computeCellLine <- function(case_id =case_id,expS...
R/computeCellLine.R:17 pick.out.cell.line <- function(expr.of.sampl...
R/computeCellLine.R:18 marker.gene <- inter...
R/computeCellLine.R:19 marker.gene <- inter...
R/computeCellLine.R:20 correlation.matrix <- cor(expr.of...
R/computeCellLine.R:22 cell.line.median.cor <- apply(correla...
* NOTE: Consider 4 spaces instead of tabs; 49 lines (3%) contain
tabs.
First 6 lines:
R/computeCellLine.R:59
R/computeCellLine.R:61
R/computeCellLine.R:62 octad.LINCS.counts=ExperimentHub()[["EH7273"]]
R/computeCellLine.R:64
R/computeCellLine.R:65 print(paste('computing correlation between cell...
R/computeCellLine.R:74
* NOTE: Consider multiples of 4 spaces for line indents, 115
lines(7%) are not.
First 6 lines:
R/computeCellLine.R:16 #helper function by Ke
R/computeRefTissue.R:8 adjacent=FALSE,
R/computeRefTissue.R:9 source='octad',n_va...
R/computeRefTissue.R:10 method='varGenes',...
R/computeRefTissue.R:11 expSet=NULL,
R/computeRefTissue.R:12 #site_selection = ...
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: 9
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output