HenrikBengtsson
commented
1 year ago There is (at least) one _R_CHECK_LENGTH_1_CONDITION_ bug and (at least) one _R_CHECK_LENGTH_1_LOGIC2_ bug:
$ wget http://download.r-forge.r-project.org/src/contrib/mpcbs_1.1.1.tar.gz
$ R CMD check --as-cran mpcbs_1.1.1.tar.gz
* using log directory ‘/home/hb/repositories/aroma.core/.local/mpcbs.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘mpcbs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mpcbs’ version ‘1.1.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Nancy R. Zhang <nzhang@stanford.edu>’
New submission
Non-FOSS package license (What license is it under?)
The Title field should be in title case. Current version is:
‘Multi-sample and Multiplatform CNV.’
In title case that is:
‘Multi-Sample and Multiplatform CNV.’
The Date field is over a month old.
This build time stamp is over a month old.
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘mpcbs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
What license is it under?
Standardizable: FALSE
* 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 ... OK
* checking S3 generic/method consistency ... WARNING
merge:
function(x, y, ...)
merge.pos:
function(pos, anchors)
plot:
function(x, ...)
plot.crossplatform:
function(pos, y, anchor, chpts, ranking, yhat, platform.names,
num.panels, xlim, ...)
update:
function(object, ...)
update.bic.baseline:
function(this.y, segbag, carriers, this.sum.deltasq,
this.sum.deltasqwin, newchpt, samp.ord, win, y.var,
PRIOR.CARRIER.PROB, PRIOR.SEGCOUNT, do.plots)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
merge.pos plot.crossplatform update.bic.baseline
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s/11s] NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
Chisq.Contrib.test: no visible global function definition for ‘runif’
Chisq.Contrib.test: no visible global function definition for ‘par’
Chisq.Contrib.test: no visible global function definition for ‘image’
ComputeZ.R: no visible binding for global variable ‘y’
Remove.Overlap.test: no visible global function definition for ‘par’
Remove.Overlap.test: no visible global function definition for ‘runif’
Remove.Overlap.test: no visible global function definition for ‘image’
compute.var: no visible binding for global variable ‘median’
compute.var: no visible global function definition for ‘median’
computeBeta: no visible global function definition for ‘integrate’
computeMoments: no visible global function definition for ‘integrate’
computeZ.onechange: no visible global function definition for ‘pchisq’
computeZ.onechange.sample: no visible global function definition for
‘pchisq’
computeZ.squarewave.sample: no visible global function definition for
‘pchisq’
computeZ.test: no visible global function definition for ‘par’
computeZ.test: no visible global function definition for ‘rnorm’
computeZ.test: no visible binding for global variable ‘z’
computeZ.test: no visible global function definition for ‘image’
fcompute.max.Z: no visible binding for global variable ‘var’
fscan.max: no visible global function definition for ‘lines’
fscan.max: no visible global function definition for ‘points’
fscan.max: no visible binding for global variable ‘MIN.SNPS’
getCutoffEpidemicChangeLocationKnown: no visible global function
definition for ‘qchisq’
mpcbs: no visible global function definition for ‘pdf’
mpcbs: no visible global function definition for ‘par’
mpcbs: no visible global function definition for ‘segments’
mpcbs: no visible global function definition for ‘dev.off’
mpcbs.mbic: no visible global function definition for ‘pdf’
mpcbs.mbic: no visible global function definition for ‘par’
mpcbs.mbic: no visible global function definition for ‘segments’
mpcbs.mbic: no visible global function definition for ‘dev.off’
mpscan: no visible global function definition for ‘par’
mpscan: no visible global function definition for ‘lines’
mpscan: no visible global function definition for ‘segments’
plot.crossplatform: no visible global function definition for ‘par’
plot.crossplatform: no visible global function definition for ‘lines’
plot.crossplatform: no visible global function definition for
‘segments’
plot.crossplatform: no visible global function definition for ‘text’
pvalueMultisampleWeightedChisq: no visible global function definition
for ‘integrate’
pvalueMultisampleWeightedChisqold: no visible global function
definition for ‘integrate’
pvalueSumChisq: no visible global function definition for ‘integrate’
scatter.ci: no visible global function definition for ‘segments’
scatter.ci: no visible global function definition for ‘points’
scatter.cpfit: no visible global function definition for ‘par’
scatter.cpfit: no visible binding for global variable ‘sd’
scatter.cpfit: no visible global function definition for ‘abline’
scatter.cpfit: no visible global function definition for ‘points’
update.bic.baseline: no visible global function definition for ‘par’
update.bic.baseline: no visible global function definition for ‘points’
update.bic.baseline: no visible global function definition for
‘segments’
vu: no visible global function definition for ‘pnorm’
wpca: no visible global function definition for ‘lm’
wpca: no visible global function definition for ‘par’
wpca: no visible global function definition for ‘abline’
wpca: no visible global function definition for ‘points’
wpca: no visible global function definition for ‘lines’
wpca: no visible global function definition for ‘legend’
Undefined global functions or variables:
MIN.SNPS abline dev.off image integrate legend lines lm median par
pchisq pdf pnorm points qchisq rnorm runif sd segments text var y z
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "abline", "image", "legend", "lines", "par",
"points", "segments", "text")
importFrom("stats", "integrate", "lm", "median", "pchisq", "pnorm",
"qchisq", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'cross.platform.consensus.Rd':
\examples lines wider than 100 characters:
consensus.cn = res$consensus.cn[[1]] # consensus.cn[t] is consensus copy number estimate at anchor$merged.pos[t]
plot.crossplatform(pos,y, yhat=seg$yhat, anchor=anchor,platform.names=platform.names, num.panels=K+1, col="darkgray")
plot.crossplatform(pos,y, yhat=seg$yhat, anchor=anchor,platform.names=platform.names, num.panels=K+1, xlim=c(xmin,xmax), col="darkgray" ... [TRUNCATED]
Rd file 'mpcbs-package.Rd':
\examples lines wider than 100 characters:
consensus.cn = res$consensus.cn[[1]] # consensus.cn[t] is consensus copy number estimate at anchor$merged.pos[t]
plot.crossplatform(pos,y, yhat=seg$yhat, anchor=anchor,platform.names=platform.names, num.panels=K+1, col="darkgray")
plot.crossplatform(pos,y, yhat=seg$yhat, anchor=anchor,platform.names=platform.names, num.panels=K+1, xlim=c(xmin,xmax), col="darkgray" ... [TRUNCATED]
xlab="Genome Position", ylab="Log Ratio", main="Consensus Copy Number Estimate", cex.lab=2, xlim=c(xmin,xmax))
Rd file 'mpcbs.Rd':
\examples lines wider than 100 characters:
#plot.crossplatform(pos,y, yhat=seg$yhat, chpts=seg$chpts, anchor=anchor, platform.names=platform.names, col="darkgray")
Rd file 'mpcbs.mbic.Rd':
\examples lines wider than 100 characters:
plot.crossplatform(pos,y, yhat=seg$yhat, chpts=seg$chpts, anchor=anchor, platform.names=platform.names, col="darkgray")
Rd file 'plot.crossplatform.Rd':
\usage lines wider than 90 characters:
plot.crossplatform(pos, y, anchor, chpts = NULL, ranking = NULL, yhat = NULL, platform.names, num.panels = NA, xlim = NULL, ...)
\examples lines wider than 100 characters:
plot.crossplatform(pos,y, yhat=seg$yhat, anchor=anchor, platform.names=platform.names, col="darkgray")
plot.crossplatform(pos,y, yhat=seg$yhat, chpts=seg$chpts, anchor=anchor, platform.names=platform.names, col="darkgray")
plot.crossplatform(pos,y, yhat=seg$yhat, chpts=seg$chpts, anchor=anchor, platform.names=platform.names, col="darkgray", xlim=c(5e7,1e8) ... [TRUNCATED]
plot.crossplatform(pos,y, yhat=seg$yhat, chpts=seg$chpts, anchor=anchor, platform.names=platform.names, col="darkgray", xlim=c(5e7,6e7) ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘ComputeProjectedZ.fromS.R.segments’
Undocumented data sets:
‘mpcbs.example’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Variables with usage in documentation object 'mpcbsexample' but not in code:
‘mpcbsexample’
Codoc mismatches from documentation object 'compute.var':
compute.var
Code: function(y, use.mean = TRUE)
Docs: function(y)
Argument names in code not in docs:
use.mean
Codoc mismatches from documentation object 'merge.pos':
merge.pos
Code: function(pos, anchors = NULL)
Docs: function(pos, anchors = 1)
Mismatches in argument default values:
Name: 'anchors' Code: NULL Docs: 1
Codoc mismatches from documentation object 'mpcbs':
mpcbs
Code: function(y, pos, anchor, win, Z = NULL, MIN.SNPs = 2,
MIN.BP.LEN = 10000, ALPHA = 0, rratio = NULL, f =
NULL, MAX.CHPTS = 50, WCHISQ.CUTOFF = NA,
platform.names = NULL, plots = TRUE, plotspdf = NULL,
use.filtered.scan = TRUE, useProjectedChisquare =
TRUE)
Docs: function(y, pos, anchors)
Argument names in code not in docs:
anchor win Z MIN.SNPs MIN.BP.LEN ALPHA rratio f MAX.CHPTS
WCHISQ.CUTOFF platform.names plots plotspdf use.filtered.scan
useProjectedChisquare
Argument names in docs not in code:
anchors
Mismatches in argument names:
Position: 3 Code: anchor Docs: anchors
Codoc mismatches from documentation object 'mpcbs.mbic':
mpcbs.mbic
Code: function(y, pos, anchor, MIN.SNPs = 2, MIN.BP.LEN = 1000,
rratio = NULL, f = NULL, MAX.CHPTS = 30,
platform.names = NULL, plots = TRUE, plotspdf = NULL,
use.filtered.scan = TRUE)
Docs: function(y, pos, anchor, MIN.SNPs = 2, MAX.CHPTS = 30,
platform.names, plots = TRUE)
Argument names in code not in docs:
MIN.BP.LEN rratio f plotspdf use.filtered.scan
Mismatches in argument names:
Position: 5 Code: MIN.BP.LEN Docs: MAX.CHPTS
Position: 6 Code: rratio Docs: platform.names
Position: 7 Code: f Docs: plots
Mismatches in argument default values:
Name: 'platform.names' Code: NULL Docs:
Codoc mismatches from documentation object 'mpscan':
mpscan
Code: function(y, pos, anchors, win, Z = NULL, MIN.SNPs = 1, ALPHA =
0, WCHISQ.CUTOFF = NA)
Docs: function(y, pos, anchors, win)
Argument names in code not in docs:
Z MIN.SNPs ALPHA WCHISQ.CUTOFF
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'compute.var':
‘use.mean’
Undocumented arguments in documentation object 'mpcbs'
‘anchors’
Documented arguments not in \usage in documentation object 'mpcbs':
‘anchor’ ‘MIN.SNPs’ ‘MIN.BP.LEN’ ‘WCHISQ.CUTOFF’ ‘rratio’
‘platform.names’ ‘plots’ ‘plotspdf’ ‘use.filtered.scan’
Documented arguments not in \usage in documentation object 'mpcbs.mbic':
‘MIN.BP.LEN’ ‘rratio’ ‘plotspdf’ ‘use.filtered.scan’
Undocumented arguments in documentation object 'mpscan'
‘anchors’
Documented arguments not in \usage in documentation object 'mpscan':
‘anchor’ ‘MIN.SNPs’ ‘WCHISQ.CUTOFF’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'merge.pos':
‘merge.pos’
S3 methods shown with full name in documentation object 'plot.crossplatform':
‘plot.crossplatform’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘mpcbs/libs/mpcbs.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... ERROR
Running examples in ‘mpcbs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cross.platform.consensus
> ### Title: Compute the cross platform consensus copy number given a
> ### segmentation.
> ### Aliases: cross.platform.consensus
> ### Keywords: weighted least squares
>
> ### ** Examples
>
>
> data(mpcbs.example)
>
> # there are 3 platforms represented in this data example: Illumina, Affymetrix, and Agilent.
> names(mpcbs.example)
[1] "illu" "affy" "agil"
>
> # K is the number of platforms.
> K=3
>
> # Store the chromosome positions in vector pos,
> # the intensities in vector y:
>
> pos=vector("list",K)
> pos[[1]] = mpcbs.example$illu[,1]
> pos[[2]] = mpcbs.example$affy[,1]
> pos[[3]] = mpcbs.example$agil[,1]
>
> y = vector("list",K)
> y[[1]] = mpcbs.example$illu[,2]
> y[[2]] = mpcbs.example$affy[,2]
> y[[3]] = mpcbs.example$agil[,2]
>
> # Names of the platforms:
> platform.names=c("Illumina","Affymetrix","Agilent")
>
> # Get the anchor set.
> anchor = merge.pos(pos)
>
> # Perform the segmentation.
> seg<-mpcbs.mbic(y,pos,anchor, MAX.CHPTS=10, platform.names=platform.names,plots=TRUE)
Using anchors containing 142404 positions.
Use filtered scan: TRUE , maximum change-points: 10
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
mpcbs
--- call from context ---
fcompute.max.ProjectedZ(S, SST, imap, win, rratio, MIN.SNPs,
f = f)
--- call from argument ---
is.na(rratio) || (length(rratio) != K)
--- R stacktrace ---
where 1: fcompute.max.ProjectedZ(S, SST, imap, win, rratio, MIN.SNPs,
f = f)
where 2: mpcbs.mbic(y, pos, anchor, MAX.CHPTS = 10, platform.names = platform.names,
plots = TRUE)
--- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
--- function from context ---
function (this.S, this.SST, this.imap, win, rratio, MIN.SNPs,
f = NULL)
{
K = ncol(this.S)
this.T = nrow(this.S)
if (is.na(rratio) || (length(rratio) != K)) {
rratio = rep(1, K)
}
win = min(win, this.T - 1)
temp = fscan.max(this.S, this.SST, this.imap = this.imap,
MIN.SNPs = MIN.SNPs, rratio = rratio, f = f, use.Project.statistic = TRUE,
verbose = FALSE)
bestchpt = temp$seg
bestZ = temp$maxZ
list(bestchpt = bestchpt, bestZ = bestZ)
}
<bytecode: 0x55ad735e2ba0>
<environment: namespace:mpcbs>
--- function search by body ---
Function fcompute.max.ProjectedZ in namespace mpcbs has this body.
----------- END OF FAILURE REPORT --------------
Error in is.na(rratio) || (length(rratio) != K) :
'length(x) = 3 > 1' in coercion to 'logical(1)'
Calls: mpcbs.mbic -> fcompute.max.ProjectedZ
Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 5 NOTEs
See
‘/home/hb/repositories/aroma.core/.local/mpcbs.Rcheck/00check.log’
for details.
From R-hub checks: