##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PharmacoGx_3.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PharmacoGx.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘3.3.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PharmacoGx’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 R 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 ... NOTE
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’
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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
PharmacoSet-accessors 4.086  1.236   5.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CreatingPharmacoSet.Rmd’ using ‘UTF-8’... OK
  ‘DetectingDrugSynergyAndAntagonism.Rmd’ using ‘UTF-8’... OK
  ‘PharmacoGx.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
--- finished re-building ‘CreatingPharmacoSet.Rmd’

--- re-building ‘DetectingDrugSynergyAndAntagonism.Rmd’ using rmarkdown
Killed
--- re-building ‘PharmacoGx.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PharmacoGx.Rcheck/vign_test/PharmacoGx/vignettes/PharmacoGx_files/figure-html/fig1-1.png" but not available.
--- finished re-building ‘PharmacoGx.Rmd’

SUMMARY: processing the following file failed:
  ‘DetectingDrugSynergyAndAntagonism.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘PharmacoGx’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c metaPermC.c -o metaPermC.o
metaPermC.c: In function ‘runPerm’:
metaPermC.c:143:12: warning: unused variable ‘num_larger’ [-Wunused-variable]
  143 |   uint64_t num_larger = 0;
      |            ^~~~~~~~~~
metaPermC.c: In function ‘partialCorQUICKSTOP’:
metaPermC.c:328:10: warning: unused variable ‘temp’ [-Wunused-variable]
  328 |   double temp;
      |          ^~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rCPP_bridge.cpp -o rCPP_bridge.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-PharmacoGx/00new/PharmacoGx/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PharmacoGx)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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, sort, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[1]  1  1 -1
[1] 0
[1] 0
             [,1] [,2] [,3]
lower_bounds    0    0    0
upper_bounds    1    1   -1

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

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

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
 96.546   0.605  97.299