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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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 760/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
garfield 1.35.0  (landing page)
Valentina Iotchkova
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/garfield
git_branch: devel
git_last_commit: ff65122
git_last_commit_date: 2024-10-29 10:07:39 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for garfield on kjohnson3

To the developers/maintainers of the garfield package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/garfield.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: garfield
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:garfield.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings garfield_1.35.0.tar.gz
StartedAt: 2024-12-23 19:22:09 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:22:21 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 12.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: garfield.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:garfield.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings garfield_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/garfield.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘garfield/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘garfield’ version ‘1.35.0’
* 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 ‘garfield’ can be installed ... WARNING
Found the following significant warnings:
  garfield_perm.cpp:306:74: warning: format specifies type 'char *' but the argument has type 'long' [-Wformat]
  garfield_perm.cpp:306:78: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
  garfield_perm.cpp:306:86: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
  garfield_perm.cpp:306:110: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
  garfield_perm.cpp:306:117: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
  garfield_perm.cpp:356:16: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
  garfield_prep.cpp:262:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/garfield.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
garfield.plot: no visible global function definition for ‘read.table’
garfield.plot: no visible global function definition for
  ‘colorRampPalette’
garfield.plot: no visible global function definition for ‘pdf’
garfield.plot: no visible global function definition for ‘layout’
garfield.plot: no visible global function definition for ‘par’
garfield.plot: no visible global function definition for ‘title’
garfield.plot: no visible global function definition for ‘legend’
garfield.plot: no visible global function definition for ‘dev.off’
garfield.plot.fnx: no visible global function definition for ‘par’
garfield.plot.fnx: no visible global function definition for ‘polygon’
garfield.plot.fnx: no visible global function definition for ‘segments’
garfield.plot.fnx: no visible global function definition for ‘points’
garfield.plot.fnx: no visible global function definition for ‘lines’
garfield.plot.fnx: no visible global function definition for ‘median’
garfield.plot.fnx: no visible global function definition for ‘text’
Undefined global functions or variables:
  colorRampPalette dev.off layout legend lines median par pdf points
  polygon read.table segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "layout", "legend", "lines", "par", "points",
             "polygon", "segments", "text", "title")
  importFrom("stats", "median")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/garfield/libs/garfield.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/garfield.Rcheck/00check.log’
for details.


Installation output

garfield.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL garfield
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘garfield’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c garfield_init.c -o garfield_init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c garfield_perm.cpp -o garfield_perm.o
garfield_perm.cpp:306:74: warning: format specifies type 'char *' but the argument has type 'long' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                           ~~                                                          ^~~
                           %ld
garfield_perm.cpp:306:78: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                              ~~                                                           ^~~~~~
                              %d
garfield_perm.cpp:306:86: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                    ~~                                                             ^~~~~~~~~~~~~~~~~~~~~~
                                    %f
garfield_perm.cpp:306:27: warning: invalid conversion specifier '\x09' [-Wformat-invalid-specifier]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                      ~~^
garfield_perm.cpp:306:110: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                            ~~                                                                             ^~~~~~
                                            %d
garfield_perm.cpp:306:117: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                                                                 ~~                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                 %f
garfield_perm.cpp:356:16: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
                Rprintf("%s",nannot);
                         ~~  ^~~~~~
                         %d
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c garfield_prep.cpp -o garfield_prep.o
garfield_prep.cpp:262:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
                                annot1[i] = annot1[i] | annot2[i];
                                            ^~~~~~~~~~~~~~~~~~~~~
                                                      ||
garfield_prep.cpp:262:17: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o garfield.so garfield_init.o garfield_perm.o garfield_prep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-garfield/00new/garfield/libs
** R
** 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 (garfield)

Tests output


Example timings

garfield.Rcheck/garfield-Ex.timings

nameusersystemelapsed
garfield.plot1.2380.0681.311
garfield.plot.fnx0.0020.0010.001
garfield.run0.3300.0070.337