Drop {mpcbs} tests and examples, because that package is broken in R (>= 4.2.0) #29
Milestone
Comments
HenrikBengtsson
changed the title
|
There is (at least) one $ 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. |
HenrikBengtsson
added a commit
that referenced
this issue
Nov 10, 2022
HenrikBengtsson
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
From R-hub checks:
The text was updated successfully, but these errors were encountered: