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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2033/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Structstrings 1.21.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/Structstrings
git_branch: devel
git_last_commit: 3bba55a
git_last_commit_date: 2024-04-30 11:13:11 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for Structstrings on palomino4

To the developers/maintainers of the Structstrings package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Structstrings.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: Structstrings
Version: 1.21.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Structstrings.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Structstrings_1.21.0.tar.gz
StartedAt: 2024-06-10 10:44:52 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 10:52:30 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 458.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Structstrings.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Structstrings.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Structstrings_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Structstrings.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'Structstrings/DESCRIPTION' ... OK
* this is package 'Structstrings' version '1.21.0'
* 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 'Structstrings' can be installed ... WARNING
Found the following significant warnings:
  DotBracketDataFrame_class.c:40:29: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
  DotBracketDataFrame_class.c:40:31: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
  DotBracketDataFrame_class.c:52:25: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
  DotBracketDataFrame_class.c:52:27: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/Structstrings.Rcheck/00install.out' for details.
* used C compiler: 'gcc.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
Unexported objects imported by ':::' calls:
  'Biostrings:::.XStringSet.show_frame_header'
  'S4Vectors:::new_SimpleList_from_list'
  See the note in ?`:::` about the use of this operator.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* 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 'F:/biocbuild/bbs-3.20-bioc/R/library/Structstrings/libs/x64/Structstrings.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (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
getBasePairing 5.37   0.09    5.48
* 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: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/Structstrings.Rcheck/00check.log'
for details.


Installation output

Structstrings.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Structstrings
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Structstrings' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DotBracketDataFrame_class.c -o DotBracketDataFrame_class.o
DotBracketDataFrame_class.c: In function 'get_base_pairing_per_char_pair':
DotBracketDataFrame_class.c:40:29: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
   40 |         error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close);
      |                            ~^                                        ~~~~~~~~~~~~
      |                             |                                        |
      |                             char *                                   int
      |                            %d
DotBracketDataFrame_class.c:40:31: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
   40 |         error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close);
      |                              ~^                                                    ~~~~~~~~~~~~~
      |                               |                                                    |
      |                               char *                                               int
      |                              %d
DotBracketDataFrame_class.c:52:25: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
   52 |     error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open,  bracket_close);
      |                        ~^                                        ~~~~~~~~~~~~
      |                         |                                        |
      |                         char *                                   int
      |                        %d
DotBracketDataFrame_class.c:52:27: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
   52 |     error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open,  bracket_close);
      |                          ~^                                                     ~~~~~~~~~~~~~
      |                           |                                                     |
      |                           char *                                                int
      |                          %d
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_Structstrings.c -o R_init_Structstrings.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
gcc -shared -s -static-libgcc -o Structstrings.dll tmp.def DotBracketDataFrame_class.o IRanges_stubs.o R_init_Structstrings.o S4Vectors_stubs.o utils.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-Structstrings/00new/Structstrings/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 (Structstrings)

Tests output

Structstrings.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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.

> library(testthat)
> library(Structstrings)
Loading required package: S4Vectors
Loading required package: stats4
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


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: Biostrings
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_check("Structstrings")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 174 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 174 ]
> 
> proc.time()
   user  system elapsed 
  95.29   11.26  106.70 

Example timings

Structstrings.Rcheck/Structstrings-Ex.timings

nameusersystemelapsed
DotBracketDataFrame1.250.281.56
DotBracketString0.060.000.06
DotBracketStringSet-io1.160.071.22
LoopIndexList0.070.000.07
Structstrings-internals2.210.062.27
StructuredXStringSet0.040.000.05
convertAnnotation0.040.000.03
getBasePairing5.370.095.48