Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:41:24 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2200/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TypeInfo 1.68.0  (landing page)
Duncan Temple Lang
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/TypeInfo
git_branch: RELEASE_3_18
git_last_commit: 8933d6d
git_last_commit_date: 2023-10-24 09:36:52 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for TypeInfo on kunpeng2


To the developers/maintainers of the TypeInfo package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TypeInfo.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: TypeInfo
Version: 1.68.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings TypeInfo_1.68.0.tar.gz
StartedAt: 2023-11-02 15:08:02 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 15:08:24 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:   OK  
CheckDir: TypeInfo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings TypeInfo_1.68.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TypeInfo.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TypeInfo/DESCRIPTION’ ... OK
* this is package ‘TypeInfo’ version ‘1.68.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TypeInfo’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  BSD_2_clause
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘copyEnv.R’
  Running ‘copySubstitute.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/TypeInfo.Rcheck/00check.log’
for details.



Installation output

TypeInfo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL TypeInfo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘TypeInfo’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TypeInfo)

Tests output

TypeInfo.Rcheck/tests/copyEnv.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Biobase)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(TypeInfo)
> typeInfo( copyEnv ) <-
+      SimultaneousTypeSpecification(
+          TypedSignature(
+             oldEnv = "environment" ,
+             newEnv = "environment" ,
+             all.names = "logical"
+         ),
+         returnType = "vector")
> 
> proc.time()
   user  system elapsed 
  0.858   0.061   0.907 

TypeInfo.Rcheck/tests/copySubstitute.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TypeInfo)
> require(Biobase)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> copySubstitute <- Biobase::copySubstitute
> 
> 
> typeInfo( copySubstitute ) <-
+     IndependentTypeSpecification(
+             src = c("character", "connection"),
+             dest = expression(is(dest, class(src))),
+             symbolValues = "list" ,
+             symbolDelimiter = expression(is.character(symbolDelimiter) &&
+                 length(symbolDelimiter) == 1 &&
+                 all(nchar(symbolDelimiter) == 1)),
+             allowUnresolvedSymbols = "logical" ,
+             recursive = "logical" ,
+             removeExtension = "character",
+             returnType = "NULL")
> 
> 
> infile  = tempfile()
> outfile = tempfile()
> 
> writeLines(text=c("We will perform in @WHAT@:",
+   "So, thanks to @WHOM@ at once and to each one,",
+   "Whom we invite to see us crown'd at @WHERE@."),
+   con = infile)
> 
> ## create the symbol table
> z = list(WHAT="measure, time and place", WHOM="all", WHERE="Scone")
> 
> ## run copySubstitute
> copySubstitute(infile, outfile, z)
NULL
> 
> cat("Next call should be an error\n")
Next call should be an error
> ## should be caught, but is not
> tryCatch({
+   copySubstitute(123, outfile, z);
+   stop("should have caught that!")
+   }, error=function(err) {})
NULL
> 
> proc.time()
   user  system elapsed 
  0.961   0.033   0.981 

Example timings

TypeInfo.Rcheck/TypeInfo-Ex.timings

nameusersystemelapsed
DynamicTypeTest-class0.0220.0000.022
IndependentTypeSpecification-class0.0480.0000.048
IndependentTypeSpecification0.0240.0000.024
NamedTypeTest-class0.0030.0000.003
ReturnTypeSpecification0.0040.0000.004
SimultaneousTypeSpecification0.010.000.01
TypedSignature0.0020.0000.002
checkArgs000
hasParameterType0.0110.0000.011
rewriteTypeCheck000
showTypeInfo0.0010.0020.004