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This page was generated on 2024-05-04 11:39:48 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1701/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.40.0  (landing page)
Nan Xiao
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_19
git_last_commit: ce83e55
git_last_commit_date: 2024-04-30 10:35:37 -0400 (Tue, 30 Apr 2024)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.40.0
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: 2024-05-04 00:18:41 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:21:20 -0400 (Sat, 04 May 2024)
EllapsedTime: 159.4 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 beta (2024-04-14 r86421)
* 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 ‘1.40.0’
* 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 beta (2024-04-14 r86421) -- "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 
  8.071   0.800   7.885 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0010.0020.004
AA3DMoRSE0.0020.0020.004
AAACF0.0010.0010.003
AABLOSUM1000.0010.0010.002
AABLOSUM450.0010.0020.003
AABLOSUM500.0010.0020.002
AABLOSUM620.0010.0010.003
AABLOSUM800.0000.0010.002
AABurden0.0010.0010.002
AACPSA0.0010.0010.002
AAConn0.0010.0000.002
AAConst0.0010.0010.001
AADescAll0.0000.0010.002
AAEdgeAdj0.0010.0000.002
AAEigIdx0.0010.0010.001
AAFGC0.0010.0010.002
AAGETAWAY0.0010.0010.003
AAGeom0.0010.0020.003
AAInfo0.0010.0010.002
AAMOE2D0.0010.0010.002
AAMOE3D0.0010.0010.003
AAMetaInfo0.0010.0010.002
AAMolProp0.0010.0020.002
AAPAM1200.0010.0020.003
AAPAM2500.0010.0010.002
AAPAM300.0010.0010.002
AAPAM400.0010.0010.002
AAPAM700.0000.0010.002
AARDF0.0010.0010.002
AARandic0.0010.0010.002
AATopo0.0010.0010.002
AATopoChg0.0010.0020.002
AAWHIM0.0010.0020.002
AAWalk0.0010.0010.002
AAindex0.0010.0010.002
OptAA3d0.0000.0000.001
acc0.0100.0070.017
calcDrugFPSim000
calcDrugMCSSim0.0050.0050.010
calcParProtGOSim000
calcParProtSeqSim0.0060.0040.011
calcTwoProtGOSim0.0000.0010.001
calcTwoProtSeqSim0.0020.0020.004
checkProt0.0010.0010.002
convMolFormat0.0000.0010.002
extractDrugAIO0.0010.0010.001
extractDrugALOGP0.0010.0010.002
extractDrugAminoAcidCount0.0010.0010.001
extractDrugApol0.0010.0010.002
extractDrugAromaticAtomsCount0.0010.0010.001
extractDrugAromaticBondsCount0.0010.0010.001
extractDrugAtomCount0.0000.0010.001
extractDrugAutocorrelationCharge0.0010.0000.002
extractDrugAutocorrelationMass0.0010.0000.001
extractDrugAutocorrelationPolarizability0.0020.0010.002
extractDrugBCUT0.0010.0010.002
extractDrugBPol0.0010.0010.001
extractDrugBondCount0.0010.0010.002
extractDrugCPSA0.0010.0010.002
extractDrugCarbonTypes0.0010.0010.001
extractDrugChiChain0.0010.0010.002
extractDrugChiCluster0.0010.0000.002
extractDrugChiPath0.0010.0010.002
extractDrugChiPathCluster0.0010.0010.001
extractDrugDescOB0.0070.0030.011
extractDrugECI0.0000.0000.001
extractDrugEstate0.0010.0000.002
extractDrugEstateComplete0.0010.0000.001
extractDrugExtended0.0010.0010.002
extractDrugExtendedComplete0.0010.0010.001
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0010.0010.001
extractDrugGraph0.0000.0000.001
extractDrugGraphComplete0.0000.0000.001
extractDrugGravitationalIndex0.0010.0000.002
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0000.0000.001
extractDrugHybridization0.0010.0010.001
extractDrugHybridizationComplete0.0010.0010.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0000.000
extractDrugKRComplete0.0010.0010.001
extractDrugKappaShapeIndices0.0010.0000.001
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0010.001
extractDrugLargestPiSystem0.0000.0010.001
extractDrugLengthOverBreadth0.0010.0010.002
extractDrugLongestAliphaticChain0.0010.0010.001
extractDrugMACCS0.0000.0010.002
extractDrugMACCSComplete0.0010.0000.001
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0060.0030.011
extractDrugOBFP30.0150.0070.022
extractDrugOBFP40.0060.0020.007
extractDrugOBMACCS0.0150.0080.024
extractDrugPetitjeanNumber0.0010.0000.001
extractDrugPetitjeanShapeIndex0.0010.0010.001
extractDrugPubChem0.0010.0010.001
extractDrugPubChemComplete0.0010.0010.002
extractDrugRotatableBondsCount0.0010.0010.001
extractDrugRuleOfFive0.0010.0010.002
extractDrugShortestPath0.0010.0000.001
extractDrugShortestPathComplete0.0010.0010.001
extractDrugStandard0.0010.0010.001
extractDrugStandardComplete0.0000.0010.001
extractDrugTPSA0.0010.0010.002
extractDrugVABC0.0010.0010.001
extractDrugVAdjMa0.0010.0010.002
extractDrugWHIM0.0010.0010.001
extractDrugWeight0.0000.0000.002
extractDrugWeightedPath0.0010.0010.002
extractDrugWienerNumbers0.0010.0010.001
extractDrugXLogP0.0000.0010.001
extractDrugZagrebIndex0.0010.0010.001
extractPCMBLOSUM0.0100.0020.013
extractPCMDescScales0.0120.0020.015
extractPCMFAScales0.0300.0060.037
extractPCMMDSScales0.0120.0030.015
extractPCMPropScales0.0120.0030.015
extractPCMScales0.0180.0030.022
extractProtAAC0.0020.0010.004
extractProtAPAAC0.9060.0350.954
extractProtCTDC0.0030.0010.003
extractProtCTDD0.0040.0030.007
extractProtCTDT0.0050.0010.006
extractProtCTriad0.1020.0120.116
extractProtDC0.0040.0060.009
extractProtGeary0.1430.0130.158
extractProtMoran0.1430.0120.158
extractProtMoreauBroto0.1310.0110.144
extractProtPAAC0.5270.0120.544
extractProtPSSM0.0010.0010.002
extractProtPSSMAcc0.0020.0000.002
extractProtPSSMFeature0.0010.0000.002
extractProtQSO0.7730.0220.805
extractProtSOCN0.7760.0160.803
extractProtTC0.0380.0920.140
getCPI0.0020.0010.002
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0030.0020.005
getProt000
getSeqFromKEGG0.0000.0000.001
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.002
readMolFromSDF0.0010.0010.003
readMolFromSmi0.0010.0010.001
readPDB0.7000.0080.716
searchDrug0.0020.0010.003
segProt0.0020.0010.003