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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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 1164/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEDME 1.65.0  (landing page)
Mattia Pelizzola
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/MEDME
git_branch: devel
git_last_commit: 3c269cd
git_last_commit_date: 2024-04-30 10:18:43 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for MEDME on palomino6

To the developers/maintainers of the MEDME package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEDME.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: MEDME
Version: 1.65.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDME.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MEDME_1.65.0.tar.gz
StartedAt: 2024-07-16 01:29:27 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 01:31:38 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 130.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MEDME.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDME.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MEDME_1.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MEDME.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'MEDME/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDME' version '1.65.0'
* 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 'MEDME' can be installed ... OK
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'MEDME' for: 'initialize', 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CGcount: no visible binding for global variable 'Hsapiens'
CGcount: no visible binding for global variable 'Mmusculus'
CGcount: no visible global function definition for 'start'
CGcount: no visible global function definition for 'new'
MEDME: no visible global function definition for 'quantile'
MEDME: no visible global function definition for 'median'
MEDME: no visible global function definition for 'png'
MEDME: no visible global function definition for 'contour'
MEDME: no visible global function definition for 'colors'
MEDME: no visible global function definition for 'points'
MEDME: no visible global function definition for 'lines'
MEDME: no visible global function definition for 'fitted'
MEDME: no visible global function definition for 'dev.off'
MEDME.predict: no visible global function definition for 'coef'
MEDME.predict: no visible global function definition for 'new'
MEDME.readFiles: no visible global function definition for 'read.table'
MEDME.readFiles: no visible global function definition for 'new'
MEDME.writeFiles: no visible global function definition for
  'write.table'
smooth: no visible global function definition for 'new'
initialize,MEDMEset: no visible global function definition for
  'callNextMethod'
show,MEDMEset: no visible global function definition for 'show'
Undefined global functions or variables:
  Hsapiens Mmusculus callNextMethod coef colors contour dev.off fitted
  lines median new png points quantile read.table show start
  write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off", "png")
  importFrom("graphics", "contour", "lines", "points")
  importFrom("methods", "callNextMethod", "new", "show")
  importFrom("stats", "coef", "fitted", "median", "quantile", "start")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'MEDMEset,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/MEDME/libs/x64/MEDME.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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
CGcount       11.33   1.86   13.18
MEDME.predict  4.15   2.60    6.77
MEDME          4.25   0.78    5.05
* 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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/MEDME.Rcheck/00check.log'
for details.


Installation output

MEDME.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MEDME
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'MEDME' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MEDMEweight.c -o MEDMEweight.o
MEDMEweight.c: In function 'MEDMEweight':
MEDMEweight.c:90:33: warning: 'B' may be used uninitialized [-Wmaybe-uninitialized]
   90 |       AMSfinal[i] = pow(2, pow( pow(E,B) * (D - Mlim) / (Mlim - C), 1/B));
      |                                 ^~~~~~~~
MEDMEweight.c:36:10: note: 'B' was declared here
   36 |   double B,C,D,E, Min, Max, Mlim;
      |          ^
MEDMEweight.c:89:9: warning: 'C' may be used uninitialized [-Wmaybe-uninitialized]
   89 |       if(Mlim < C) {Mlim = C;}
      |         ^
MEDMEweight.c:36:12: note: 'C' was declared here
   36 |   double B,C,D,E, Min, Max, Mlim;
      |            ^
MEDMEweight.c:88:9: warning: 'D' may be used uninitialized [-Wmaybe-uninitialized]
   88 |       if(Mlim > D) {Mlim = D;} // the model is only meaningful for MeDIPw in (C,D)
      |         ^
MEDMEweight.c:36:14: note: 'D' was declared here
   36 |   double B,C,D,E, Min, Max, Mlim;
      |              ^
MEDMEweight.c:90:33: warning: 'E' may be used uninitialized [-Wmaybe-uninitialized]
   90 |       AMSfinal[i] = pow(2, pow( pow(E,B) * (D - Mlim) / (Mlim - C), 1/B));
      |                                 ^~~~~~~~
MEDMEweight.c:36:16: note: 'E' was declared here
   36 |   double B,C,D,E, Min, Max, Mlim;
      |                ^
MEDMEweight.c:92:9: warning: 'Min' may be used uninitialized [-Wmaybe-uninitialized]
   92 |       if(AMSfinal[i] < Min) {AMSfinal[i] = Min;}
      |         ^
MEDMEweight.c:36:19: note: 'Min' was declared here
   36 |   double B,C,D,E, Min, Max, Mlim;
      |                   ^~~
MEDMEweight.c:91:9: warning: 'Max' may be used uninitialized [-Wmaybe-uninitialized]
   91 |       if(AMSfinal[i] > Max) {AMSfinal[i] = Max;}
      |         ^
MEDMEweight.c:36:24: note: 'Max' was declared here
   36 |   double B,C,D,E, Min, Max, Mlim;
      |                        ^~~
MEDMEweight.c:78:19: warning: 'weight' may be used uninitialized [-Wmaybe-uninitialized]
   78 |         weightSum = weightSum + weight;
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
MEDMEweight.c:30:10: note: 'weight' was declared here
   30 |   double weight, relPos;
      |          ^~~~~~
gcc -shared -s -static-libgcc -o MEDME.dll tmp.def MEDMEweight.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-MEDME/00new/MEDME/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 (MEDME)

Tests output


Example timings

MEDME.Rcheck/MEDME-Ex.timings

nameusersystemelapsed
CGcount11.33 1.8613.18
MEDME4.250.785.05
MEDME.predict4.152.606.77
MEDMEset-class0.020.000.01
smooth0.110.010.14