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This page was generated on 2024-03-28 11:39:52 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1679/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.39.0  (landing page)
Nan Xiao
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: devel
git_last_commit: 59fdfc6
git_last_commit_date: 2023-10-24 09:58:01 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Rcpi on lconway


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: 1.39.0
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_1.39.0.tar.gz
StartedAt: 2024-03-27 23:29:03 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:31:37 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 153.7 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_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.39.0’
* 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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 
  7.713   0.770   7.510 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0020.004
AA3DMoRSE0.0010.0010.002
AAACF0.0010.0010.003
AABLOSUM1000.0010.0020.002
AABLOSUM450.0010.0010.002
AABLOSUM500.0010.0020.002
AABLOSUM620.0010.0010.002
AABLOSUM800.0010.0010.002
AABurden0.0010.0020.003
AACPSA0.0010.0010.002
AAConn0.0010.0010.002
AAConst0.0010.0020.002
AADescAll0.0010.0020.003
AAEdgeAdj0.0010.0010.002
AAEigIdx0.0010.0010.002
AAFGC0.0010.0010.002
AAGETAWAY0.0000.0010.002
AAGeom0.0010.0010.003
AAInfo0.0000.0010.002
AAMOE2D0.0010.0010.002
AAMOE3D0.0010.0010.002
AAMetaInfo0.0010.0010.003
AAMolProp0.0010.0010.002
AAPAM1200.0010.0010.003
AAPAM2500.0010.0010.002
AAPAM300.0000.0010.002
AAPAM400.0010.0000.002
AAPAM700.0010.0020.003
AARDF0.0010.0010.002
AARandic0.0000.0010.003
AATopo0.0010.0010.002
AATopoChg0.0010.0010.002
AAWHIM0.0010.0010.002
AAWalk0.0000.0010.002
AAindex0.0010.0010.002
OptAA3d000
acc0.0090.0060.015
calcDrugFPSim000
calcDrugMCSSim0.0050.0040.012
calcParProtGOSim000
calcParProtSeqSim0.0060.0030.011
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0020.003
checkProt0.0020.0010.002
convMolFormat0.0010.0010.002
extractDrugAIO0.0000.0010.001
extractDrugALOGP0.0010.0010.001
extractDrugAminoAcidCount0.0010.0010.002
extractDrugApol0.0010.0010.001
extractDrugAromaticAtomsCount0.0010.0010.002
extractDrugAromaticBondsCount0.0000.0010.001
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge0.0010.0010.001
extractDrugAutocorrelationMass0.0000.0010.002
extractDrugAutocorrelationPolarizability0.0010.0010.001
extractDrugBCUT0.0010.0010.002
extractDrugBPol0.0010.0010.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0010.0000.001
extractDrugChiCluster0.0010.0000.002
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0140.0080.022
extractDrugECI0.0010.0010.002
extractDrugEstate0.0010.0010.002
extractDrugEstateComplete0.0010.0010.001
extractDrugExtended0.0010.0010.001
extractDrugExtendedComplete0.0000.0010.002
extractDrugFMF0.0010.0000.002
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0000.002
extractDrugGravitationalIndex0.0000.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.002
extractDrugHybridization0.0000.0000.001
extractDrugHybridizationComplete0.0010.0010.001
extractDrugHybridizationRatio0.0010.0000.002
extractDrugIPMolecularLearning0.0000.0000.001
extractDrugKR0.0010.0000.002
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0010.001
extractDrugKierHallSmarts0.0010.0010.002
extractDrugLargestChain0.0010.0010.001
extractDrugLargestPiSystem0.0000.0010.001
extractDrugLengthOverBreadth0.0010.0000.002
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0010.0010.001
extractDrugMACCSComplete0.0010.0000.002
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0000.002
extractDrugMomentOfInertia0.0000.0000.001
extractDrugOBFP20.0070.0020.009
extractDrugOBFP30.0150.0070.022
extractDrugOBFP40.0080.0040.012
extractDrugOBMACCS0.0930.0070.101
extractDrugPetitjeanNumber0.0000.0000.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0010.003
extractDrugPubChemComplete0.0010.0010.001
extractDrugRotatableBondsCount0.0010.0000.001
extractDrugRuleOfFive0.0010.0000.002
extractDrugShortestPath0.0000.0010.001
extractDrugShortestPathComplete0.0010.0010.002
extractDrugStandard0.0010.0010.002
extractDrugStandardComplete0.0010.0010.001
extractDrugTPSA0.0000.0010.001
extractDrugVABC0.0010.0010.002
extractDrugVAdjMa0.0010.0010.001
extractDrugWHIM0.0010.0010.001
extractDrugWeight0.0010.0010.002
extractDrugWeightedPath0.0010.0010.001
extractDrugWienerNumbers0.0010.0010.001
extractDrugXLogP0.0000.0010.001
extractDrugZagrebIndex0.0010.0010.001
extractPCMBLOSUM0.0100.0020.012
extractPCMDescScales0.0130.0020.016
extractPCMFAScales0.0180.0050.023
extractPCMMDSScales0.0110.0030.014
extractPCMPropScales0.0210.0030.024
extractPCMScales0.0170.0030.021
extractProtAAC0.0020.0010.003
extractProtAPAAC0.8860.0360.934
extractProtCTDC0.0020.0010.003
extractProtCTDD0.0040.0020.006
extractProtCTDT0.0060.0010.008
extractProtCTriad0.1010.0120.114
extractProtDC0.0040.0040.007
extractProtGeary0.1570.0130.172
extractProtMoran0.1320.0100.144
extractProtMoreauBroto0.4480.0130.466
extractProtPAAC0.4100.0100.425
extractProtPSSM0.0020.0010.002
extractProtPSSMAcc0.0020.0000.002
extractProtPSSMFeature0.0020.0010.002
extractProtQSO0.7100.0230.745
extractProtSOCN0.7390.0160.766
extractProtTC0.0340.0860.121
getCPI0.0030.0010.004
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS0.0000.0000.001
getMolFromChEMBL0.0000.0000.001
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0020.0020.004
getProt0.0000.0010.000
getSeqFromKEGG000
getSeqFromRCSBPDB0.0010.0000.000
getSeqFromUniProt0.0000.0010.000
getSmiFromChEMBL000
getSmiFromDrugBank0.0000.0010.000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0010.001
readFASTA0.0010.0010.002
readMolFromSDF0.0020.0020.004
readMolFromSmi0.0010.0010.002
readPDB0.8220.0140.848
searchDrug0.0020.0020.003
segProt0.0020.0020.004