Multiple platform build/check report for BioC 3.19 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4466
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*

CHECK results for Rcpi on merida1

To the developers/maintainers of the Rcpi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rcpi.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.

raw results

Summary

Package: Rcpi

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rcpi_1.40.0.tar.gz

StartedAt: 2024-06-24 10:09:08 -0400 (Mon, 24 Jun 2024)

EndedAt: 2024-06-24 10:14:26 -0400 (Mon, 24 Jun 2024)

EllapsedTime: 318.0 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rcpi_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.40.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
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 ‘Rcpi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 code 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 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 ... NOTE
checkRd: (-1) AAMetaInfo.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AAMetaInfo.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AAMetaInfo.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AAMetaInfo.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AAMetaInfo.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AAMetaInfo.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) acc.Rd:42: Lost braces
    42 | Wold, S., Jonsson, J., Sj\"{o}rstr\"{o}m, M., Sandberg,
       |                            ^
checkRd: (-1) acc.Rd:42: Lost braces
    42 | Wold, S., Jonsson, J., Sj\"{o}rstr\"{o}m, M., Sandberg,
       |                                     ^
checkRd: (-1) acc.Rd:43: Lost braces
    43 | M., & R\"{a}nnar, S. (1993).
       |          ^
checkRd: (-1) acc.Rd:49: Lost braces
    49 | Sj\"{o}str\"{o}m, M., R\"{a}nnar, S., & Wieslander, A. (1995).
       |     ^
checkRd: (-1) acc.Rd:49: Lost braces
    49 | Sj\"{o}str\"{o}m, M., R\"{a}nnar, S., & Wieslander, A. (1995).
       |             ^
checkRd: (-1) acc.Rd:49: Lost braces
    49 | Sj\"{o}str\"{o}m, M., R\"{a}nnar, S., & Wieslander, A. (1995).
       |                          ^
checkRd: (-1) extractProtPSSMAcc.Rd:39: Lost braces
    39 | Wold, S., Jonsson, J., Sj\"{o}rstr\"{o}m, M., Sandberg,
       |                            ^
checkRd: (-1) extractProtPSSMAcc.Rd:39: Lost braces
    39 | Wold, S., Jonsson, J., Sj\"{o}rstr\"{o}m, M., Sandberg,
       |                                     ^
checkRd: (-1) extractProtPSSMAcc.Rd:40: Lost braces
    40 | M., & R\"{a}nnar, S. (1993).
       |          ^
checkRd: (-1) readFASTA.Rd:40: Lost braces; missing escapes or markup?
    40 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) readFASTA.Rd:40: Lost braces; missing escapes or markup?
    40 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck/00check.log’
for details.

Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Rcpi’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (Rcpi)

Tests output

Rcpi.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(testthat)
> library(Rcpi)

> 
> test_check("Rcpi")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 14.387   1.151  15.618

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.003	0.002	0.006
AA3DMoRSE	0.001	0.002	0.005
AAACF	0.001	0.002	0.004
AABLOSUM100	0.002	0.003	0.004
AABLOSUM45	0.002	0.002	0.007
AABLOSUM50	0.002	0.002	0.004
AABLOSUM62	0.001	0.002	0.005
AABLOSUM80	0.002	0.002	0.005
AABurden	0.002	0.002	0.005
AACPSA	0.002	0.002	0.005
AAConn	0.001	0.002	0.003
AAConst	0.002	0.002	0.006
AADescAll	0.002	0.002	0.004
AAEdgeAdj	0.001	0.002	0.007
AAEigIdx	0.001	0.002	0.006
AAFGC	0.002	0.002	0.003
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.001	0.003	0.005
AAInfo	0.002	0.003	0.004
AAMOE2D	0.002	0.003	0.004
AAMOE3D	0.002	0.002	0.006
AAMetaInfo	0.002	0.002	0.003
AAMolProp	0.001	0.002	0.005
AAPAM120	0.002	0.002	0.003
AAPAM250	0.002	0.002	0.006
AAPAM30	0.001	0.002	0.004
AAPAM40	0.002	0.002	0.007
AAPAM70	0.002	0.002	0.004
AARDF	0.002	0.002	0.004
AARandic	0.002	0.002	0.004
AATopo	0.001	0.002	0.004
AATopoChg	0.002	0.002	0.004
AAWHIM	0.001	0.002	0.004
AAWalk	0.002	0.002	0.005
AAindex	0.002	0.002	0.005
OptAA3d	0	0	0
acc	0.018	0.017	0.038
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.007	0.007	0.058
calcParProtGOSim	0.000	0.001	0.001
calcParProtSeqSim	0.009	0.005	0.019
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.004	0.001	0.006
checkProt	0.002	0.001	0.003
convMolFormat	0.002	0.001	0.003
extractDrugAIO	0.001	0.000	0.002
extractDrugALOGP	0.002	0.001	0.002
extractDrugAminoAcidCount	0.001	0.001	0.002
extractDrugApol	0.001	0.000	0.002
extractDrugAromaticAtomsCount	0.002	0.001	0.003
extractDrugAromaticBondsCount	0.001	0.000	0.003
extractDrugAtomCount	0.001	0.001	0.002
extractDrugAutocorrelationCharge	0.002	0.001	0.002
extractDrugAutocorrelationMass	0.001	0.001	0.002
extractDrugAutocorrelationPolarizability	0.002	0.001	0.003
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.001	0.000	0.003
extractDrugBondCount	0.002	0.001	0.002
extractDrugCPSA	0.001	0.001	0.003
extractDrugCarbonTypes	0.001	0.000	0.003
extractDrugChiChain	0.001	0.001	0.002
extractDrugChiCluster	0.002	0.000	0.002
extractDrugChiPath	0.001	0.001	0.002
extractDrugChiPathCluster	0.002	0.001	0.003
extractDrugDescOB	0.011	0.008	0.024
extractDrugECI	0.001	0.001	0.002
extractDrugEstate	0.002	0.001	0.005
extractDrugEstateComplete	0.001	0.001	0.002
extractDrugExtended	0.002	0.001	0.003
extractDrugExtendedComplete	0.001	0.000	0.002
extractDrugFMF	0.002	0.001	0.003
extractDrugFragmentComplexity	0.002	0.001	0.002
extractDrugGraph	0.001	0.001	0.002
extractDrugGraphComplete	0.002	0.001	0.003
extractDrugGravitationalIndex	0.001	0.001	0.003
extractDrugHBondAcceptorCount	0.002	0.001	0.003
extractDrugHBondDonorCount	0.001	0.000	0.002
extractDrugHybridization	0.002	0.001	0.002
extractDrugHybridizationComplete	0.001	0.001	0.002
extractDrugHybridizationRatio	0.002	0.001	0.002
extractDrugIPMolecularLearning	0.002	0.001	0.003
extractDrugKR	0.002	0.000	0.002
extractDrugKRComplete	0.001	0.001	0.003
extractDrugKappaShapeIndices	0.001	0.001	0.002
extractDrugKierHallSmarts	0.002	0.001	0.003
extractDrugLargestChain	0.001	0.001	0.003
extractDrugLargestPiSystem	0.002	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.000	0.002
extractDrugLongestAliphaticChain	0.001	0.001	0.003
extractDrugMACCS	0.002	0.000	0.003
extractDrugMACCSComplete	0.001	0.001	0.002
extractDrugMDE	0.001	0.001	0.002
extractDrugMannholdLogP	0.002	0.001	0.003
extractDrugMomentOfInertia	0.001	0.000	0.002
extractDrugOBFP2	0.011	0.006	0.024
extractDrugOBFP3	0.019	0.010	0.032
extractDrugOBFP4	0.011	0.006	0.022
extractDrugOBMACCS	0.018	0.008	0.027
extractDrugPetitjeanNumber	0.002	0.001	0.002
extractDrugPetitjeanShapeIndex	0.001	0.001	0.002
extractDrugPubChem	0.002	0.001	0.004
extractDrugPubChemComplete	0.001	0.000	0.002
extractDrugRotatableBondsCount	0.002	0.001	0.002
extractDrugRuleOfFive	0.001	0.001	0.003
extractDrugShortestPath	0.002	0.001	0.002
extractDrugShortestPathComplete	0.002	0.001	0.003
extractDrugStandard	0.001	0.001	0.002
extractDrugStandardComplete	0.002	0.001	0.003
extractDrugTPSA	0.001	0.000	0.002
extractDrugVABC	0.001	0.001	0.002
extractDrugVAdjMa	0.002	0.001	0.004
extractDrugWHIM	0.002	0.001	0.002
extractDrugWeight	0.001	0.000	0.003
extractDrugWeightedPath	0.002	0.001	0.002
extractDrugWienerNumbers	0.001	0.001	0.002
extractDrugXLogP	0.001	0.001	0.003
extractDrugZagrebIndex	0.002	0.001	0.003
extractPCMBLOSUM	0.017	0.004	0.023
extractPCMDescScales	0.018	0.003	0.025
extractPCMFAScales	0.131	0.008	0.160
extractPCMMDSScales	0.018	0.005	0.025
extractPCMPropScales	0.020	0.003	0.029
extractPCMScales	0.031	0.006	0.043
extractProtAAC	0.003	0.001	0.004
extractProtAPAAC	1.847	0.057	2.199
extractProtCTDC	0.004	0.001	0.006
extractProtCTDD	0.008	0.005	0.016
extractProtCTDT	0.007	0.002	0.010
extractProtCTriad	0.197	0.024	0.271
extractProtDC	0.008	0.013	0.022
extractProtGeary	0.686	0.028	0.841
extractProtMoran	0.297	0.025	0.376
extractProtMoreauBroto	0.292	0.025	0.408
extractProtPAAC	1.211	0.041	1.474
extractProtPSSM	0.002	0.001	0.003
extractProtPSSMAcc	0.002	0.001	0.004
extractProtPSSMFeature	0.002	0.001	0.003
extractProtQSO	2.283	0.087	2.674
extractProtSOCN	2.249	0.030	2.685
extractProtTC	0.088	0.265	0.382
getCPI	0.003	0.003	0.007
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.005	0.004	0.008
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.001	0.000	0.000
getSmiFromChEMBL	0.001	0.000	0.000
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.000	0.001	0.000
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.002	0.001	0.004
readMolFromSDF	0.005	0.002	0.010
readMolFromSmi	0.001	0.000	0.004
readPDB	1.387	0.021	1.664
searchDrug	0.003	0.001	0.004
segProt	0.004	0.004	0.010