Multiple platform build/check report for BioC 3.20 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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: 1.41.0

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_1.41.0.tar.gz

StartedAt: 2024-06-10 08:34:53 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 08:40:10 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 317.9 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_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.41.0’
* 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-3.20-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 Patched (2024-04-24 r86482) -- "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 
 14.083   1.141  14.739

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.004	0.003	0.006
AA3DMoRSE	0.002	0.003	0.005
AAACF	0.002	0.003	0.005
AABLOSUM100	0.002	0.003	0.008
AABLOSUM45	0.002	0.003	0.006
AABLOSUM50	0.001	0.003	0.004
AABLOSUM62	0.002	0.002	0.005
AABLOSUM80	0.002	0.002	0.004
AABurden	0.002	0.002	0.006
AACPSA	0.002	0.002	0.004
AAConn	0.002	0.002	0.005
AAConst	0.001	0.003	0.005
AADescAll	0.002	0.002	0.006
AAEdgeAdj	0.002	0.003	0.004
AAEigIdx	0.002	0.002	0.005
AAFGC	0.001	0.002	0.004
AAGETAWAY	0.001	0.002	0.004
AAGeom	0.002	0.002	0.005
AAInfo	0.002	0.002	0.006
AAMOE2D	0.001	0.002	0.004
AAMOE3D	0.002	0.002	0.010
AAMetaInfo	0.002	0.002	0.003
AAMolProp	0.001	0.002	0.006
AAPAM120	0.002	0.002	0.006
AAPAM250	0.002	0.002	0.004
AAPAM30	0.002	0.002	0.004
AAPAM40	0.001	0.002	0.004
AAPAM70	0.001	0.003	0.005
AARDF	0.002	0.002	0.006
AARandic	0.002	0.002	0.003
AATopo	0.001	0.002	0.004
AATopoChg	0.002	0.002	0.005
AAWHIM	0.002	0.002	0.004
AAWalk	0.002	0.002	0.006
AAindex	0.002	0.002	0.005
OptAA3d	0.000	0.001	0.001
acc	0.019	0.021	0.048
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.007	0.007	0.298
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.009	0.006	0.895
calcTwoProtGOSim	0.000	0.001	0.021
calcTwoProtSeqSim	0.003	0.001	0.004
checkProt	0.002	0.001	0.003
convMolFormat	0.015	0.003	0.021
extractDrugAIO	0.001	0.001	0.004
extractDrugALOGP	0.002	0.001	0.003
extractDrugAminoAcidCount	0.001	0.001	0.003
extractDrugApol	0.002	0.001	0.003
extractDrugAromaticAtomsCount	0.002	0.001	0.002
extractDrugAromaticBondsCount	0.001	0.001	0.002
extractDrugAtomCount	0.002	0.001	0.002
extractDrugAutocorrelationCharge	0.001	0.001	0.003
extractDrugAutocorrelationMass	0.002	0.001	0.003
extractDrugAutocorrelationPolarizability	0.001	0.001	0.002
extractDrugBCUT	0.001	0.001	0.003
extractDrugBPol	0.002	0.001	0.003
extractDrugBondCount	0.001	0.001	0.011
extractDrugCPSA	0.002	0.001	0.002
extractDrugCarbonTypes	0.001	0.001	0.002
extractDrugChiChain	0.001	0.001	0.002
extractDrugChiCluster	0.001	0.000	0.002
extractDrugChiPath	0.002	0.000	0.002
extractDrugChiPathCluster	0.001	0.000	0.003
extractDrugDescOB	0.011	0.008	0.335
extractDrugECI	0.002	0.001	0.003
extractDrugEstate	0.001	0.001	0.003
extractDrugEstateComplete	0.001	0.001	0.004
extractDrugExtended	0.002	0.001	0.003
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.002	0.001	0.004
extractDrugFragmentComplexity	0.002	0.001	0.002
extractDrugGraph	0.001	0.001	0.003
extractDrugGraphComplete	0.001	0.001	0.003
extractDrugGravitationalIndex	0.002	0.000	0.002
extractDrugHBondAcceptorCount	0.001	0.001	0.003
extractDrugHBondDonorCount	0.001	0.000	0.004
extractDrugHybridization	0.002	0.001	0.003
extractDrugHybridizationComplete	0.002	0.000	0.002
extractDrugHybridizationRatio	0.001	0.002	0.008
extractDrugIPMolecularLearning	0.002	0.001	0.003
extractDrugKR	0.002	0.002	0.002
extractDrugKRComplete	0.001	0.000	0.003
extractDrugKappaShapeIndices	0.002	0.001	0.002
extractDrugKierHallSmarts	0.001	0.001	0.003
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.001	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.001	0.002
extractDrugLongestAliphaticChain	0.002	0.001	0.003
extractDrugMACCS	0.001	0.001	0.002
extractDrugMACCSComplete	0.002	0.001	0.002
extractDrugMDE	0.002	0.001	0.004
extractDrugMannholdLogP	0.001	0.001	0.003
extractDrugMomentOfInertia	0.001	0.001	0.002
extractDrugOBFP2	0.011	0.007	0.021
extractDrugOBFP3	0.016	0.005	0.021
extractDrugOBFP4	0.012	0.007	0.019
extractDrugOBMACCS	0.016	0.007	0.023
extractDrugPetitjeanNumber	0.002	0.001	0.003
extractDrugPetitjeanShapeIndex	0.001	0.001	0.002
extractDrugPubChem	0.002	0.001	0.004
extractDrugPubChemComplete	0.002	0.001	0.004
extractDrugRotatableBondsCount	0.002	0.002	0.004
extractDrugRuleOfFive	0.002	0.001	0.002
extractDrugShortestPath	0.001	0.001	0.002
extractDrugShortestPathComplete	0.002	0.001	0.003
extractDrugStandard	0.002	0.001	0.003
extractDrugStandardComplete	0.001	0.001	0.004
extractDrugTPSA	0.001	0.001	0.002
extractDrugVABC	0.002	0.001	0.005
extractDrugVAdjMa	0.001	0.001	0.003
extractDrugWHIM	0.002	0.001	0.002
extractDrugWeight	0.002	0.000	0.002
extractDrugWeightedPath	0.001	0.001	0.004
extractDrugWienerNumbers	0.002	0.000	0.002
extractDrugXLogP	0.001	0.001	0.002
extractDrugZagrebIndex	0.002	0.001	0.002
extractPCMBLOSUM	0.018	0.005	0.024
extractPCMDescScales	0.017	0.004	0.036
extractPCMFAScales	0.133	0.013	0.149
extractPCMMDSScales	0.018	0.004	0.024
extractPCMPropScales	0.022	0.006	0.028
extractPCMScales	0.033	0.006	0.039
extractProtAAC	0.003	0.002	0.006
extractProtAPAAC	1.745	0.068	2.057
extractProtCTDC	0.003	0.002	0.005
extractProtCTDD	0.008	0.007	0.020
extractProtCTDT	0.009	0.003	0.015
extractProtCTriad	0.196	0.027	0.228
extractProtDC	0.008	0.018	0.039
extractProtGeary	0.665	0.033	0.710
extractProtMoran	0.286	0.030	0.328
extractProtMoreauBroto	0.294	0.031	0.341
extractProtPAAC	1.127	0.042	1.187
extractProtPSSM	0.002	0.001	0.004
extractProtPSSMAcc	0.002	0.002	0.004
extractProtPSSMFeature	0.002	0.002	0.005
extractProtQSO	2.192	0.086	2.374
extractProtSOCN	2.155	0.033	2.214
extractProtTC	0.086	0.320	0.473
getCPI	0.004	0.005	0.010
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.001	0.001	0.001
getFASTAFromUniProt	0.001	0.001	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0.000	0.001	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.000	0.001	0.001
getPPI	0.005	0.007	0.020
getProt	0.000	0.001	0.001
getSeqFromKEGG	0.000	0.001	0.002
getSeqFromRCSBPDB	0.000	0.000	0.002
getSeqFromUniProt	0.000	0.001	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.000	0.001	0.000
getSmiFromPubChem	0.001	0.001	0.002
readFASTA	0.002	0.002	0.005
readMolFromSDF	0.004	0.002	0.005
readMolFromSmi	0.002	0.001	0.007
readPDB	1.345	0.022	2.059
searchDrug	0.003	0.002	0.011
segProt	0.005	0.005	0.010