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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1508/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PharmacoGx 3.9.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/PharmacoGx
git_branch: devel
git_last_commit: e7ed1c4
git_last_commit_date: 2024-04-30 10:53:08 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  


CHECK results for PharmacoGx on palomino6

To the developers/maintainers of the PharmacoGx package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PharmacoGx.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: PharmacoGx
Version: 3.9.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PharmacoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PharmacoGx_3.9.0.tar.gz
StartedAt: 2024-07-16 02:43:00 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 02:49:35 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 395.0 seconds
RetCode: 0
Status:   OK  
CheckDir: PharmacoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PharmacoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PharmacoGx_3.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/PharmacoGx.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PharmacoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PharmacoGx' version '3.9.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'PharmacoGx' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.Hill' '.summarizeSensitivityNumbers' 'partialCorQUICKSTOP'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.computeZIPdelta: no visible binding for global variable
  'EC50_proj_1_to_2'
.computeZIPdelta: no visible binding for global variable
  'EC50_proj_2_to_1'
.computeZIPdelta: no visible binding for global variable
  'HS_proj_1_to_2'
.computeZIPdelta: no visible binding for global variable
  'HS_proj_2_to_1'
.computeZIPdelta: no visible binding for global variable
  'E_inf_proj_2_to_1'
.computeZIPdelta: no visible binding for global variable
  'E_inf_proj_1_to_2'
.computeZIPdelta: no visible binding for global variable 'Rsqr_1_to_2'
.computeZIPdelta: no visible binding for global variable 'Rsqr_2_to_1'
.plotProjHill: no visible binding for global variable 'treatment1id'
.plotProjHill: no visible binding for global variable 'treatment2id'
.plotProjHill: no visible binding for global variable 'treatment2dose'
.plotProjHill: no visible binding for global variable
  'EC50_proj_2_to_1'
.plotProjHill: no visible binding for global variable 'HS_proj_2_to_1'
.plotProjHill: no visible binding for global variable 'EC50_2'
.plotProjHill: no visible binding for global variable 'E_inf_2'
.plotProjHill: no visible binding for global variable
  'E_inf_proj_2_to_1'
.plotProjHill: no visible binding for global variable 'HS_2'
.plotProjHill: no visible binding for global variable 'treatment1dose'
.plotProjHill: no visible binding for global variable 'combo_viability'
.plotProjHill: no visible binding for global variable 'x'
.plotProjHill: no visible binding for global variable
  'EC50_proj_1_to_2'
.plotProjHill: no visible binding for global variable 'HS_proj_1_to_2'
.plotProjHill: no visible binding for global variable 'EC50_1'
.plotProjHill: no visible binding for global variable 'HS_1'
.plotProjHill: no visible binding for global variable 'E_inf_1'
.plotProjHill: no visible binding for global variable
  'E_inf_proj_1_to_2'
PharmacoSet2: no visible global function definition for
  'MultiAssayExperiment'
fitTwowayZIP: no visible binding for global variable 'treatment1dose'
fitTwowayZIP: no visible binding for global variable 'combo_viability'
fitTwowayZIP: no visible binding for global variable 'treatment2dose'
fitTwowayZIP: no visible binding for global variable 'EC50_2'
fitTwowayZIP: no visible binding for global variable 'HS_2'
fitTwowayZIP: no visible binding for global variable 'E_inf_2'
fitTwowayZIP: no visible binding for global variable 'EC50_1'
fitTwowayZIP: no visible binding for global variable 'HS_1'
fitTwowayZIP: no visible binding for global variable 'E_inf_1'
mergePSets: no visible global function definition for
  'checkPSetStructure'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'ZIP'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'EC50_proj_1_to_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'EC50_proj_2_to_1'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'EC50_1'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'EC50_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'HS_proj_1_to_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'HS_proj_2_to_1'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'HS_1'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'HS_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'E_inf_1'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'E_inf_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'E_inf_proj_2_to_1'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'E_inf_proj_1_to_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'treatment1dose'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'treatment2dose'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'Rsqr_1_to_2'
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable 'Rsqr_2_to_1'
Undefined global functions or variables:
  EC50_1 EC50_2 EC50_proj_1_to_2 EC50_proj_2_to_1 E_inf_1 E_inf_2
  E_inf_proj_1_to_2 E_inf_proj_2_to_1 HS_1 HS_2 HS_proj_1_to_2
  HS_proj_2_to_1 MultiAssayExperiment Rsqr_1_to_2 Rsqr_2_to_1 ZIP
  checkPSetStructure combo_viability treatment1dose treatment1id
  treatment2dose treatment2id x
* checking Rd files ... OK
* 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 ... NOTE
  Note: found 2251 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/PharmacoGx/libs/x64/PharmacoGx.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
PharmacoSet-accessors 4.94   1.56    6.50
connectivityScore     2.47   0.06   12.49
gwc                   1.55   0.02   10.98
mcc                   0.86   0.00   12.30
cosinePerm            0.81   0.02   11.23
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.


Installation output

PharmacoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'PharmacoGx' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c metaPermC.c -o metaPermC.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rCPP_bridge.cpp -o rCPP_bridge.o
g++ -std=gnu++17 -shared -s -static-libgcc -o PharmacoGx.dll tmp.def RcppExports.o metaPermC.o rCPP_bridge.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-PharmacoGx/00new/PharmacoGx/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (PharmacoGx)

Tests output

PharmacoGx.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> Sys.unsetenv("R_TESTS")
> 
> library(testthat)
> library(PharmacoGx)
Loading required package: CoreGx
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'PharmacoGx'

The following objects are masked from 'package:CoreGx':

    .parseToRoxygen, amcc, connectivityScore, cosinePerm, gwc, mcc

> 
> test_check("PharmacoGx")

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[1]  1  1 -1
[1] 0
[1] 0
             [,1] [,2] [,3]
lower_bounds    0    0    0
upper_bounds    1    1   -1

  |                                                                            
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  |======================================================================| 100%

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  |                                                                            
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  |======================================================================| 100%
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_PharmacoSet_utils.R:28:1'

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
  58.54    2.28   61.00 

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
PharmacoSet-accessors4.941.566.50
PharmacoSet-utils1.060.061.12
PharmacoSet000
PharmacoSet21.550.051.60
PharmacoSig0.010.030.05
amcc0.020.000.01
availablePSets000
callingWaterfall000
checkPsetStructure0.720.030.75
computeABC0.580.090.67
computeAUC0.280.000.28
computeAmax0.260.020.29
computeBliss000
computeHSA000
computeICn0.580.000.57
computeLoewe000
computeSlope000
computeZIP000
computeZIPdelta-TreatmentResponseExperiment-method000
computeZIPdelta000
connectivityScore 2.47 0.0612.49
cosinePerm 0.81 0.0211.23
dot-computeZIPdelta000
downloadPSet000
downloadPertSig000
drugDoseResponseCurve000
drugPerturbationSig1.480.041.53
drugSensitivitySig-PharmacoSet-method0.850.020.86
effectToDose000
filterNoisyCurves0.820.030.86
fitTwowayZIP000
geneDrugSensitivity000
geneDrugSensitivityPBCorr000
geneDrugSensitivityPCorr000
gwc 1.55 0.0210.98
hillCurve000
intersectPSet0.840.030.87
loeweCI000
logLogisticRegression0.250.020.27
mcc 0.86 0.0012.30
plot.PharmacoSig1.050.091.14
show-PharmacoSet-method0.700.030.75
show-PharmacoSig-method0.850.221.07
showSigAnnot-PharmacoSig-method0.860.050.94
sub-PharmacoSet-ANY-ANY-ANY-method0.750.050.80
subsetTo-PharmacoSet-method0.780.010.80
summarizeMolecularProfiles-PharmacoSet-method0.090.000.09
summarizeSensitivityProfiles-PharmacoSet-method0.050.020.06
updateObject-PharmacoSet-method0.050.030.08