Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/BiocCheck |
| Branch: RELEASE_3_6 |
| Last Commit: 37c5e15 |
| Last Changed Date: 2017-10-30 12:40:13 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:24:06 -0400 (Thu, 12 Apr 2018).
| Package 121/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocCheck 1.14.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BiocCheck |
| Version: 1.14.0 |
| Command: rm -rf BiocCheck.buildbin-libdir BiocCheck.Rcheck && mkdir BiocCheck.buildbin-libdir BiocCheck.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocCheck.buildbin-libdir BiocCheck_1.14.0.tar.gz >BiocCheck.Rcheck\00install.out 2>&1 && cp BiocCheck.Rcheck\00install.out BiocCheck-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocCheck.buildbin-libdir --install="check:BiocCheck-install.out" --force-multiarch --no-vignettes --timings BiocCheck_1.14.0.tar.gz |
| StartedAt: 2018-04-11 22:28:46 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:31:21 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 154.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocCheck.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf BiocCheck.buildbin-libdir BiocCheck.Rcheck && mkdir BiocCheck.buildbin-libdir BiocCheck.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocCheck.buildbin-libdir BiocCheck_1.14.0.tar.gz >BiocCheck.Rcheck\00install.out 2>&1 && cp BiocCheck.Rcheck\00install.out BiocCheck-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocCheck.buildbin-libdir --install="check:BiocCheck-install.out" --force-multiarch --no-vignettes --timings BiocCheck_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocCheck.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocCheck/DESCRIPTION' ... OK
* this is package 'BiocCheck' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'codetoolsBioC'
* 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 'BiocCheck' can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Unexported objects imported by ':::' calls:
'knitr:::detect_pattern' 'tools:::RdTags'
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 ... NOTE
checkValidDevelopmentURL: no visible global function definition for
'url.exists'
Undefined global functions or variables:
url.exists
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BiocCheck 4.22 0.07 5.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BiocCheck 4.11 0.1 5.5
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocCheck.Rcheck/00check.log'
for details.
BiocCheck.Rcheck/00install.out
install for i386
* installing *source* package 'BiocCheck' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'BiocCheck'
finding HTML links ... done
BiocCheck html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'BiocCheck' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocCheck' as BiocCheck_1.14.0.zip
* DONE (BiocCheck)
In R CMD INSTALL
In R CMD INSTALL
|
BiocCheck.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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.
> BiocGenerics:::testPackage("BiocCheck")
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* ERROR: Remove whitespace from DESCRIPTION field names.
* Checking for blank lines in DESCRIPTION...
* ERROR: Remove blank lines from DESCRIPTION.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* ERROR: Package directory 'unitTestTempDir' must match Package:
field (got 'Foo').
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* ERROR: Package directory 'unitTestTempDir' must match Package:
field (got '').
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: Authors@R must evaluate to 'person' object.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: Must have one author with maintainer (cre) role.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: No Maintainer or Authors@R field in DESCRIPTION file.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: No email address in Maintainer field.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking that biocViews are present...
* ERROR: No biocViews terms found.
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* WARNING: 'foo' is an invalid BiocViews term.
* WARNING: 'Cancer' is an invalid BiocViews term.
* WARNING: 'bar' is an invalid BiocViews term. Did you mean: 'ag'
* WARNING: 'baz' is an invalid BiocViews term. Did you mean: 'ag'
* Checking for recommended biocViews...
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData)
* ERROR: Use 'parallel' instead of 'multicore'. 'multicore' is
deprecated and does not work on Windows.
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
baddep.Rd
* Checking if other packages can import this one...
* ERROR: Packages providing 1 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
package::object (function)
RJSONIO::isValidJSON (baddep)
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 2 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
object (function)
R (has_devel)
colone (iambad)
Loading required namespace: knitr
Found browser() in R/morecode.R (line 1, column 12)
Found @ in
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Remove generated comments from man pages a.Rd, baddep.Rd
* ERROR: Version number in tarball filename must match Version
field in DESCRIPTION. (Tip: create tarball with R CMD build)
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
First 1 lines:
R/morebadcode.R:2 # this is a really long line with many characters in ...
* NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
tabs.
First 2 lines:
man/a.Rd:48 ##-- or do help(data=index) for the standard data sets.
man/baddep.Rd:41 ##-- or do help(data=index) for the standard data sets.
* NOTE: Consider multiples of 4 spaces for line indents, 1
lines(0%) are not.
First 1 lines:
R/morebadcode.R:6 # something other than a multiple of 5 spaces!
See http://bioconductor.org/developers/how-to/coding-style/
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
not be included in Bioconductor release announcements.
* ERROR: New package version starting with 0.99.* (e.g., 0.99.0,
0.99.1, ...); got '1.2.3'.
* WARNING: Update R version dependency from 1.0.0 to 3.4.
* WARNING: Register native routines; see
http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
Found T in R/morecode.R (line 10, column 8)
Found F in R/morecode.R (line 7, column 5)
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* NOTE: skip_on_bioc() found in testthat files: a_test.R
* ERROR: Invalid package Version, see
http://www.bioconductor.org/developers/how-to/version-numbering/
* ERROR: Invalid package Version, see
http://www.bioconductor.org/developers/how-to/version-numbering/
* WARNING: y of x.y.z version should be even in release
* ERROR: No 'vignettes' directory.
* ERROR: No vignette sources in vignettes/ directory.
# of chunks: 0, # of eval=FALSE: 0 (0%)
* WARNING: Remove vignette sources from inst/doc; they belong in
vignettes/.
# of chunks: 0, # of eval=FALSE: 0 (0%)
* WARNING: Remove vignette sources from inst/doc; they belong in
vignettes/.
# of chunks: 0, # of eval=FALSE: 0 (0%)
# of chunks: 0, # of eval=FALSE: 0 (0%)
# of chunks: 2, # of eval=FALSE: 1 (50%)
* WARNING: Evaluate more vignette chunks.
RUNIT TEST PROTOCOL -- Wed Apr 11 22:30:39 2018
***********************************************
Number of test functions: 29
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocCheck RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
25.67 4.12 38.82
|
BiocCheck.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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.
> BiocGenerics:::testPackage("BiocCheck")
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* ERROR: Remove whitespace from DESCRIPTION field names.
* Checking for blank lines in DESCRIPTION...
* ERROR: Remove blank lines from DESCRIPTION.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* ERROR: Package directory 'unitTestTempDir' must match Package:
field (got 'Foo').
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* ERROR: Package directory 'unitTestTempDir' must match Package:
field (got '').
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: Authors@R must evaluate to 'person' object.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: Must have one author with maintainer (cre) role.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: No Maintainer or Authors@R field in DESCRIPTION file.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: No email address in Maintainer field.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking that biocViews are present...
* ERROR: No biocViews terms found.
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* WARNING: 'foo' is an invalid BiocViews term.
* WARNING: 'Cancer' is an invalid BiocViews term.
* WARNING: 'bar' is an invalid BiocViews term. Did you mean: 'ag'
* WARNING: 'baz' is an invalid BiocViews term. Did you mean: 'ag'
* Checking for recommended biocViews...
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData)
* ERROR: Use 'parallel' instead of 'multicore'. 'multicore' is
deprecated and does not work on Windows.
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
baddep.Rd
* Checking if other packages can import this one...
* ERROR: Packages providing 1 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
package::object (function)
RJSONIO::isValidJSON (baddep)
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 2 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
object (function)
R (has_devel)
colone (iambad)
Loading required namespace: knitr
Found browser() in R/morecode.R (line 1, column 12)
Found @ in
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Remove generated comments from man pages a.Rd, baddep.Rd
* ERROR: Version number in tarball filename must match Version
field in DESCRIPTION. (Tip: create tarball with R CMD build)
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
First 1 lines:
R/morebadcode.R:2 # this is a really long line with many characters in ...
* NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
tabs.
First 2 lines:
man/a.Rd:48 ##-- or do help(data=index) for the standard data sets.
man/baddep.Rd:41 ##-- or do help(data=index) for the standard data sets.
* NOTE: Consider multiples of 4 spaces for line indents, 1
lines(0%) are not.
First 1 lines:
R/morebadcode.R:6 # something other than a multiple of 5 spaces!
See http://bioconductor.org/developers/how-to/coding-style/
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
not be included in Bioconductor release announcements.
* ERROR: New package version starting with 0.99.* (e.g., 0.99.0,
0.99.1, ...); got '1.2.3'.
* WARNING: Update R version dependency from 1.0.0 to 3.4.
* WARNING: Register native routines; see
http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
Found T in R/morecode.R (line 10, column 8)
Found F in R/morecode.R (line 7, column 5)
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* NOTE: skip_on_bioc() found in testthat files: a_test.R
* ERROR: Invalid package Version, see
http://www.bioconductor.org/developers/how-to/version-numbering/
* ERROR: Invalid package Version, see
http://www.bioconductor.org/developers/how-to/version-numbering/
* WARNING: y of x.y.z version should be even in release
* ERROR: No 'vignettes' directory.
* ERROR: No vignette sources in vignettes/ directory.
# of chunks: 0, # of eval=FALSE: 0 (0%)
* WARNING: Remove vignette sources from inst/doc; they belong in
vignettes/.
# of chunks: 0, # of eval=FALSE: 0 (0%)
* WARNING: Remove vignette sources from inst/doc; they belong in
vignettes/.
# of chunks: 0, # of eval=FALSE: 0 (0%)
# of chunks: 0, # of eval=FALSE: 0 (0%)
# of chunks: 2, # of eval=FALSE: 1 (50%)
* WARNING: Evaluate more vignette chunks.
RUNIT TEST PROTOCOL -- Wed Apr 11 22:31:17 2018
***********************************************
Number of test functions: 29
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocCheck RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
22.95 3.40 38.39
|
|
BiocCheck.Rcheck/examples_i386/BiocCheck-Ex.timings
|
BiocCheck.Rcheck/examples_x64/BiocCheck-Ex.timings
|