Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2024-03-28 11:38:41 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 2170/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.47.0  (landing page)
Julius Muller
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: devel
git_last_commit: e5622ac
git_last_commit_date: 2023-10-24 09:51:41 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for TransView on palomino3


To the developers/maintainers of the TransView package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.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: TransView
Version: 1.47.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TransView.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TransView_1.47.0.tar.gz
StartedAt: 2024-03-28 07:35:16 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 07:38:40 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 204.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TransView.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TransView.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TransView_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/TransView.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 'TransView/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TransView' version '1.47.0'
* 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 whether package 'TransView' can be installed ... WARNING
Found the following significant warnings:
  parse_sam.c:161:75: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  parse_sam.c:161:103: warning: format '%d' expects argument of type 'int', but argument 4 has type 'uint32_t *' {aka 'unsigned int *'} [-Wformat=]
  parse_sam.c:202:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  parse_sam.c:203:33: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  parse_sam.c:314:61: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  parse_sam.c:314:94: warning: format '%d' expects argument of type 'int', but argument 6 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
See 'F:/biocbuild/bbs-3.19-bioc/meat/TransView.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2
* 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
'library' or 'require' call to 'RUnit' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gene2window : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
.gene2window: no visible binding for global variable 'approx'
.onAttach: no visible global function definition for
  'packageDescription'
.test: no visible global function definition for 'defineTestSuite'
.test: no visible global function definition for 'runTestSuite'
.test: no visible global function definition for 'printTextProtocol'
annotatePeaks : <anonymous>: no visible global function definition for
  'median'
gtf2gr: no visible global function definition for 'read.table'
gtf2gr: no visible global function definition for 'ave'
macs2gr: no visible global function definition for 'read.delim'
meltPeak: no visible global function definition for 'approx'
meltPeak: no visible global function definition for 'lowess'
plotTV: no visible global function definition for 'quantile'
plotTV: no visible global function definition for 'kmeans'
plotTV: no visible global function definition for 'as.dendrogram'
plotTV: no visible global function definition for 'hclust'
plotTV: no visible global function definition for 'as.dist'
plotTV: no visible global function definition for 'dist'
plotTV: no visible global function definition for 'order.dendrogram'
plotTV: no visible global function definition for 'par'
plotTV: no visible global function definition for 'layout'
plotTV: no visible global function definition for 'image'
plotTV: no visible global function definition for 'hist'
plotTV: no visible global function definition for 'title'
plotTV: no visible global function definition for 'mtext'
plotTV: no visible global function definition for 'lines'
plotTV: no visible global function definition for 'axis'
plotTV: no visible global function definition for 'rainbow'
plotTV: no visible global function definition for 'text'
plotTV: no visible global function definition for 'rgb'
plotTV: no visible global function definition for 'plot.new'
setTV: no visible global function definition for 'object.size'
.setTV,DensityContainer-character-character-numeric-numeric-numeric-logical-character-character-logical:
  no visible global function definition for 'object.size'
Undefined global functions or variables:
  approx as.dendrogram as.dist ave axis defineTestSuite dist hclust
  hist image kmeans layout lines lowess median mtext object.size
  order.dendrogram packageDescription par plot.new printTextProtocol
  quantile rainbow read.delim read.table rgb runTestSuite text title
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "hist", "image", "layout", "lines",
             "mtext", "par", "plot.new", "text", "title")
  importFrom("stats", "approx", "as.dendrogram", "as.dist", "ave",
             "dist", "hclust", "kmeans", "lowess", "median",
             "order.dendrogram", "quantile")
  importFrom("utils", "object.size", "packageDescription", "read.delim",
             "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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/TransView/libs/x64/TransView.dll':
  Found '_assert', possibly from 'assert' (C)
  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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'TransView_unit_tests.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, 6 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/TransView.Rcheck/00check.log'
for details.


Installation output

TransView.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL TransView
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'TransView' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_TransView.c -o R_init_TransView.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam_plbuf.c -o bam_plbuf.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bin_density.c -o bin_density.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c construct_dc.c -o construct_dc.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c parse_sam.c -o parse_sam.o
parse_sam.c: In function 'quality_check':
parse_sam.c:161:75: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  161 |                         warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
      |                                                                          ~^                                 ~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |                                                |
      |                                                                           int                                              hts_pos_t {aka long long int}
      |                                                                          %lld
parse_sam.c:161:103: warning: format '%d' expects argument of type 'int', but argument 4 has type 'uint32_t *' {aka 'unsigned int *'} [-Wformat=]
  161 |                         warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
      |                                                                                                      ~^
      |                                                                                                       |
      |                                                                                                       int
      |                                                                                                      %n
parse_sam.c: In function 'print_readinfo':
parse_sam.c:202:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  202 |         printf("Pos %d\n",current_read->core.pos);
      |                     ~^    ~~~~~~~~~~~~~~~~~~~~~~
      |                      |                      |
      |                      int                    hts_pos_t {aka long long int}
      |                     %lld
parse_sam.c:203:33: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  203 |         printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos);
      |                                ~^                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                 |                                   |
      |                                 int                                 hts_pos_t {aka long long int}
      |                                %lld
parse_sam.c: In function 'seq_density':
parse_sam.c:314:61: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  314 |                         warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
      |                                                            ~^
      |                                                             |
      |                                                             int
      |                                                            %lld
  315 |                                         BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
      |                                                     ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                       |
      |                                                                       hts_pos_t {aka long long int}
parse_sam.c:314:94: warning: format '%d' expects argument of type 'int', but argument 6 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  314 |                         warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
      |                                                                                             ~^
      |                                                                                              |
      |                                                                                              int
      |                                                                                             %lld
  315 |                                         BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
  316 |                                         current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                              |
      |                                                                              hts_pos_t {aka long long int}
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:184:33: warning: 'slicep' may be used uninitialized [-Wmaybe-uninitialized]
  184 |                                 expand(slicep,new_vecp,rebuildc,wsize);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
slice_dc.c:101:22: note: 'slicep' was declared here
  101 |                 int *slicep= INTEGER_POINTER(slice);
      |                      ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c visuals.c -o visuals.o
gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-TransView/00new/TransView/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TransView)

Tests output

TransView.Rcheck/tests/TransView_unit_tests.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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.

> 
> 
> require("TransView") || stop("unable to load TransView package")
Loading required package: TransView
Loading required package: GenomicRanges
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

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
Welcome to TransView version 1.47.0

Attaching package: 'TransView'

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

    pos

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

    pos

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

    pos

[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit


RUNIT TEST PROTOCOL -- Thu Mar 28 07:38:30 2024 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.39    0.60    6.96 

Example timings

TransView.Rcheck/TransView-Ex.timings

nameusersystemelapsed
DensityContainer-class0.020.000.01
TVResults-class000
TransView-package000
annotatePeaks1.610.051.66
gtf2gr0.060.000.08
macs2gr0.050.000.05
meltPeak0.640.160.82
parseReads0.000.060.07
peak2tss0.590.050.64
plotTV0.110.090.22
plotTVData0.090.160.25
rmTV0.270.060.32
slice10.080.140.22
slice1T0.620.030.67