Sean Davis
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ACME |
| git_branch: master |
| git_last_commit: 50b4948 |
| git_last_commit_date: 2021-10-26 11:51:02 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:53 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the ACME package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ACME.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 14/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ACME 2.51.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ACME |
| Version: 2.51.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ACME.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ACME_2.51.0.tar.gz |
| StartedAt: 2022-03-17 18:25:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:26:43 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 67.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ACME.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ACME.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ACME_2.51.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ACME.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '2.51.0'
* 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 'ACME' can be installed ... WARNING
Found the following significant warnings:
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
windowChisq.c:86:20: warning: initialization of 'void * (*)()' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
See 'D:/biocbuild/bbs-3.15-bioc/meat/ACME.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 30.9Mb
sub-directories of 1Mb or more:
data 3.1Mb
extdata 27.3Mb
* 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 ... NOTE
.plotACMECalcSet: no visible global function definition for 'par'
.plotACMECalcSet: no visible global function definition for 'axis'
.plotACMECalcSet: no visible global function definition for 'abline'
.plotACMESet: no visible global function definition for 'par'
do.aGFF.calc: no visible global function definition for 'quantile'
findClosestGene: no visible binding for global variable 'refflat'
findClosestGene: no visible binding for '<<-' assignment to 'refflat'
findRegions : <anonymous>: no visible global function definition for
'median'
getRefflat: no visible global function definition for 'download.file'
getRefflat: no visible global function definition for 'read.delim'
plotgff: no visible global function definition for 'par'
plotgffcalc: no visible global function definition for 'par'
plotgffcalc: no visible global function definition for 'axis'
plotgffcalc: no visible global function definition for 'abline'
read.resultsGFF: no visible global function definition for 'read.delim'
windowChisq: no visible global function definition for 'pchisq'
write.bedGraph: no visible global function definition for 'write.table'
write.sgr: no visible global function definition for 'write.table'
plot,ACMECalcSet: no visible global function definition for 'par'
plot,ACMECalcSet: no visible global function definition for 'axis'
plot,ACMECalcSet: no visible global function definition for 'abline'
plot,ACMESet: no visible global function definition for 'par'
plot,aGFF: no visible global function definition for 'par'
plot,aGFFCalc: no visible global function definition for 'par'
plot,aGFFCalc: no visible global function definition for 'axis'
plot,aGFFCalc: no visible global function definition for 'abline'
Undefined global functions or variables:
abline axis download.file median par pchisq quantile read.delim
refflat write.table
Consider adding
importFrom("graphics", "abline", "axis", "par")
importFrom("stats", "median", "pchisq", "quantile")
importFrom("utils", "download.file", "read.delim", "write.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 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 'D:/biocbuild/bbs-3.15-bioc/R/library/ACME/libs/x64/ACME.dll':
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. 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
* 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 WARNING, 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/ACME.Rcheck/00check.log'
for details.
ACME.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ACME
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ACME' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c windowChisq.c -o windowChisq.o
windowChisq.c: In function 'windowChisq':
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
firstprobe>0) {
~~~~~~~~~~^~
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lastprobe<(na-1)) {
~~~~~~~~~^~~~~~~
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
double *xa,*xlocations,*xchivals;
^~
windowChisq.c: At top level:
windowChisq.c:86:20: warning: initialization of 'void * (*)()' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
{"windowChisq",&windowChisq,5},
^
windowChisq.c:86:20: note: (near initialization for 'callMethods[0].fun')
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ACME.dll tmp.def windowChisq.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ACME/00new/ACME/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ACME'
finding HTML links ... done
ACMECalcSet-class html
finding level-2 HTML links ... done
ACMESet-class html
aGFF-class html
aGFFCalc-class html
do.aGFF.calc html
example.agff html
findClosestGene html
findRegions html
generics html
getRefflat html
read.resultsGFF html
write.bedGraph html
write.sgr html
** 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 (ACME)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MiChip' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'spkTools' is missing or broken
done
ACME.Rcheck/ACME-Ex.timings
| name | user | system | elapsed | |
| ACMECalcSet-class | 1.26 | 0.05 | 1.31 | |
| ACMESet-class | 0.39 | 0.03 | 0.42 | |
| aGFF-class | 0.44 | 0.03 | 0.47 | |
| aGFFCalc-class | 1.04 | 0.11 | 1.15 | |
| do.aGFF.calc | 1.30 | 0.03 | 1.33 | |
| example.agff | 0.39 | 0.02 | 0.41 | |
| findClosestGene | 1.33 | 0.05 | 3.96 | |
| findRegions | 3.31 | 0.14 | 3.46 | |
| generics | 0.36 | 0.05 | 0.40 | |
| getRefflat | 0.89 | 0.08 | 4.25 | |
| read.resultsGFF | 2.70 | 0.11 | 2.82 | |
| write.bedGraph | 3.14 | 0.15 | 3.29 | |
| write.sgr | 2.46 | 0.05 | 2.50 | |