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This page was generated on 2024-05-04 11:37:02 -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 nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Rcpi_1.40.0.tar.gz
StartedAt: 2024-05-04 02:47:06 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:49:08 -0400 (Sat, 04 May 2024)
EllapsedTime: 121.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Rcpi_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck/00check.log’
for details.


Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 5 | PASS 17 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• rcdk cannot be loaded (5): 'test_extractDrugALOGP.R:2:5',
  'test_extractDrugECI.R:2:5', 'test_extractDrugRuleOfFive.R:2:5',
  'test_extractDrugTPSA.R:2:5', 'test_extractDrugXLogP.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 5 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  4.591   0.313   4.893 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0010.002
AA3DMoRSE0.0010.0000.001
AAACF0.0010.0000.001
AABLOSUM1000.0010.0000.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0010.0000.001
AABLOSUM620.0010.0000.001
AABLOSUM800.0010.0000.001
AABurden0.0000.0000.001
AACPSA0.0000.0010.000
AAConn0.0000.0010.001
AAConst0.0000.0000.001
AADescAll0.0010.0000.001
AAEdgeAdj0.0010.0010.001
AAEigIdx0.0010.0000.001
AAFGC0.0000.0010.001
AAGETAWAY0.0000.0010.001
AAGeom0.0000.0010.000
AAInfo0.0010.0000.001
AAMOE2D0.0000.0000.001
AAMOE3D0.0010.0000.001
AAMetaInfo0.0010.0000.000
AAMolProp0.0010.0000.001
AAPAM1200.0010.0000.001
AAPAM2500.0000.0000.001
AAPAM300.0000.0010.000
AAPAM400.0000.0010.001
AAPAM700.0000.0000.001
AARDF0.0010.0000.001
AARandic0.0010.0010.001
AATopo0.0010.0000.001
AATopoChg0.0000.0000.001
AAWHIM0.0010.0000.000
AAWalk0.0010.0000.001
AAindex0.0000.0010.001
OptAA3d0.0000.0000.001
acc0.0100.0010.012
calcDrugFPSim000
calcDrugMCSSim0.0090.0000.010
calcParProtGOSim0.0010.0000.001
calcParProtSeqSim0.0050.0000.006
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0000.002
checkProt0.0020.0000.002
convMolFormat0.0010.0000.001
extractDrugAIO0.0000.0000.001
extractDrugALOGP0.0010.0000.000
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0000.0000.001
extractDrugAtomCount0.0010.0000.000
extractDrugAutocorrelationCharge0.0010.0000.001
extractDrugAutocorrelationMass0.0010.0000.001
extractDrugAutocorrelationPolarizability0.0000.0000.001
extractDrugBCUT0.0010.0000.000
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0000.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0000.0000.001
extractDrugChiChain0.0010.0000.000
extractDrugChiCluster0.0010.0000.001
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0090.0080.017
extractDrugECI0.0010.0000.001
extractDrugEstate0.0010.0000.001
extractDrugEstateComplete0.0010.0000.000
extractDrugExtended0.0000.0000.001
extractDrugExtendedComplete0.0010.0000.001
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph000
extractDrugGraphComplete0.0000.0000.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization000
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR000
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0000.001
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0000.000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth0.0010.0000.001
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete000
extractDrugMDE0.0000.0010.001
extractDrugMannholdLogP0.0000.0010.001
extractDrugMomentOfInertia0.0000.0010.001
extractDrugOBFP20.1110.0050.115
extractDrugOBFP30.3100.0120.322
extractDrugOBFP40.0070.0040.011
extractDrugOBMACCS0.0020.0080.010
extractDrugPetitjeanNumber0.0000.0000.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0000.001
extractDrugPubChemComplete0.0010.0000.000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive0.0010.0000.001
extractDrugShortestPath0.0010.0000.001
extractDrugShortestPathComplete0.0010.0000.001
extractDrugStandard0.0010.0000.000
extractDrugStandardComplete000
extractDrugTPSA0.0000.0000.001
extractDrugVABC0.0010.0000.001
extractDrugVAdjMa0.0010.0000.001
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0010.0000.000
extractDrugWeightedPath000
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0000.0010.001
extractDrugZagrebIndex0.0000.0010.001
extractPCMBLOSUM0.0090.0060.016
extractPCMDescScales0.0080.0000.008
extractPCMFAScales0.0110.0040.015
extractPCMMDSScales0.0080.0000.008
extractPCMPropScales0.0060.0040.010
extractPCMScales0.0160.0000.015
extractProtAAC0.0020.0000.003
extractProtAPAAC0.6090.1000.710
extractProtCTDC0.0030.0000.003
extractProtCTDD0.0050.0000.005
extractProtCTDT0.0010.0040.004
extractProtCTriad0.0730.0120.084
extractProtDC0.0040.0040.008
extractProtGeary0.0930.0040.098
extractProtMoran0.0940.0160.109
extractProtMoreauBroto0.0840.0080.092
extractProtPAAC0.3220.0160.337
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.5510.0160.567
extractProtSOCN0.5210.0000.521
extractProtTC0.0120.1120.124
getCPI0.0030.0000.003
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL0.0010.0000.000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0000.001
getPDBFromRCSBPDB000
getPPI0.0030.0000.004
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB0.0000.0000.001
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank0.0000.0000.001
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0020.0000.002
readMolFromSDF0.0020.0000.002
readMolFromSmi0.0010.0000.001
readPDB0.7940.0960.892
searchDrug0.0020.0000.002
segProt0.0030.0000.003