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This page was generated on 2022-04-13 12:05:23 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for GCSConnection on nebbiolo2


To the developers/maintainers of the GCSConnection package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GCSConnection.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 706/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GCSConnection 1.6.0  (landing page)
Jiefei Wang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GCSConnection
git_branch: RELEASE_3_14
git_last_commit: 21952ee
git_last_commit_date: 2021-10-26 12:58:13 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GCSConnection
Version: 1.6.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GCSConnection.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GCSConnection_1.6.0.tar.gz
StartedAt: 2022-04-12 07:30:59 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:31:59 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 60.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GCSConnection.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GCSConnection.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GCSConnection_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GCSConnection.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GCSConnection/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GCSConnection’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GCSConnection’ 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 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 ... 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘GCSConnection/libs/GCSConnection.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `catch_error(r)`: An error has occured when sending a REST request(Error code: 401). 
  Either you do not have the access rights, or you have sent an invalid billing project
  
  Backtrace:
      ▆
   1. ├─testthat::expect_true(gcs_is_requester_pays("bioconductor_rp")) at test_credentials.R:21:4
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─GCSConnection::gcs_is_requester_pays("bioconductor_rp")
   5.   └─GCSConnection:::.is_requester_pays(bucket)
   6.     └─GCSConnection:::catch_error(r)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GCSConnection.Rcheck/00check.log’
for details.


Installation output

GCSConnection.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GCSConnection
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GCSConnection’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c C_interface.cpp -o C_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c altrep.cpp -o altrep.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c connection.cpp -o connection.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o GCSConnection.so C_interface.o RcppExports.o altrep.o connection.o utils.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-GCSConnection/00new/GCSConnection/libs
** R
** 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 (GCSConnection)

Tests output

GCSConnection.Rcheck/tests/testthat.Rout.fail


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(GCSConnection)
> 
> test_check("GCSConnection")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_credentials.R:21:5): requester pays ─────────────────────────────
Error in `catch_error(r)`: An error has occured when sending a REST request(Error code: 401). 
Either you do not have the access rights, or you have sent an invalid billing project

Backtrace:
    ▆
 1. ├─testthat::expect_true(gcs_is_requester_pays("bioconductor_rp")) at test_credentials.R:21:4
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─GCSConnection::gcs_is_requester_pays("bioconductor_rp")
 5.   └─GCSConnection:::.is_requester_pays(bucket)
 6.     └─GCSConnection:::catch_error(r)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

Example timings

GCSConnection.Rcheck/GCSConnection-Ex.timings

nameusersystemelapsed
authentication0.0040.0010.006
buffer_size000
gcs_connection0.0340.0030.220
gcs_cp0.0860.0030.449
gcs_dir0.4790.0611.925
gcs_rm000
names-FileClass-method0.1060.0080.114
names-FolderClass-method0.0150.0000.016
requester_pays000