[Bioc-devel] release new package bioccheck failing

----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com>
To: bioc-devel at r-project.org
Sent: Tuesday, January 20, 2015 8:49:06 AM
Subject: [Bioc-devel] release new package bioccheck failing

Hi All,

I am trying to release a package https://github.com/vinash85/GOAL in
bioconductor. But BiocCheck is failing, however it only failing in
linux
and not in MAC. And I cannot figure out reason. The package is uses
Rcpp.
Both build, CHECK is passing in linux and mac.
I am using latest R (3.1.2)
The failing message from linux by BiocCheck is:

* This is BiocCheck, version 1.2.1.
* BiocCheck is a work in progress. Output and severity of issues may
  change.
* Installing package...
* This is a software package, checking vignette directories...
    * REQUIRED: vignette sources in vignettes/ directory.
* Checking version number...
    * RECOMMENDED: y of x.y.z version should be even in release
* Checking biocViews...
    * CONSIDER: Adding some of these automatically suggested
    biocViews:
      Epigenetics
* Checking build system compatibility...
* Checking unit tests...
    * CONSIDER: Adding unit tests.  We strongly recommend them. See
      http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking native routine registration...
    * RECOMMENDED: Register native routines! see

http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
* Checking for deprecated package usage...
* Parsing R code in R directory, examples, vignettes...
* Checking for T...
* Checking for F...
* Checking for browser()...
* Checking for <<-...
* Checking for library/require of GOAL...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking function lengths........
* The longest function is 87 lines long
* The longest 5 functions are:
* generate.epieQTL.logistic() (R/simulate.eQTL.R, line 4): 87 lines
* fit.logit() (R/fit.logit.R, line 1): 27 lines
* mvrnormArma() (R/RcppExports.R, line 4): 3 lines
* find_correlation() (R/RcppExports.R, line 8): 3 lines
* filterSNP() (R/RcppExports.R, line 12): 3 lines
* Checking man pages...

** Checking exported objects have runnable examples...Error in if
(line ==
"## No test: " || insideDontTest || line == "## End(No test)") { :
missing value where TRUE/FALSE neededCalls: <Anonymous> ...
checkExportsAreDocumented -> doesManPageHaveRunnableExample ->
removeDontTestExecution halted*

This was caused by a bug that was triggered by an empty \example{} section.

Fixed in BiocCheck 1.3.5 which is now available via git or svn and will be available
tomorrow via biocLite().

BTW, your package should mention its dependency on ransampl and GSL in the SystemRequirements: field of the DESCRIPTION file and your documentation (at a minimum, the README file) should explain how to install these dependencies.

Dan
thanks in advance
regards
avi

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Bioc-devel at r-project.org mailing list
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Thanks a lot Dan for quickly addressing this. BiocCheck is now passing for
the package. I have integrated instruction to install ransampl and GSL. Is
it obvious that user will include their library path to the GCC flags? In
any case I have added an example Makevars too, to do this.

thanks
avi

On Tue, Jan 20, 2015 at 6:58 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com>
To: bioc-devel at r-project.org
Sent: Tuesday, January 20, 2015 8:49:06 AM
Subject: [Bioc-devel] release new package bioccheck failing

Hi All,

I am trying to release a package https://github.com/vinash85/GOAL in
bioconductor. But BiocCheck is failing, however it only failing in
linux
and not in MAC. And I cannot figure out reason. The package is uses
Rcpp.
Both build, CHECK is passing in linux and mac.
I am using latest R (3.1.2)
The failing message from linux by BiocCheck is:

* This is BiocCheck, version 1.2.1.
* BiocCheck is a work in progress. Output and severity of issues may
  change.
* Installing package...
* This is a software package, checking vignette directories...
    * REQUIRED: vignette sources in vignettes/ directory.
* Checking version number...
    * RECOMMENDED: y of x.y.z version should be even in release
* Checking biocViews...
    * CONSIDER: Adding some of these automatically suggested
    biocViews:
      Epigenetics
* Checking build system compatibility...
* Checking unit tests...
    * CONSIDER: Adding unit tests.  We strongly recommend them. See

http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking native routine registration...
    * RECOMMENDED: Register native routines! see

http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
* Checking for deprecated package usage...
* Parsing R code in R directory, examples, vignettes...
* Checking for T...
* Checking for F...
* Checking for browser()...
* Checking for <<-...
* Checking for library/require of GOAL...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking function lengths........
* The longest function is 87 lines long
* The longest 5 functions are:
* generate.epieQTL.logistic() (R/simulate.eQTL.R, line 4): 87 lines
* fit.logit() (R/fit.logit.R, line 1): 27 lines
* mvrnormArma() (R/RcppExports.R, line 4): 3 lines
* find_correlation() (R/RcppExports.R, line 8): 3 lines
* filterSNP() (R/RcppExports.R, line 12): 3 lines
* Checking man pages...

** Checking exported objects have runnable examples...Error in if
(line ==
"## No test: " || insideDontTest || line == "## End(No test)") { :
missing value where TRUE/FALSE neededCalls: <Anonymous> ...
checkExportsAreDocumented -> doesManPageHaveRunnableExample ->
removeDontTestExecution halted*

This was caused by a bug that was triggered by an empty \example{} section.

Fixed in BiocCheck 1.3.5 which is now available via git or svn and will be
available
tomorrow via biocLite().

BTW, your package should mention its dependency on ransampl and GSL in the
SystemRequirements: field of the DESCRIPTION file and your documentation
(at a minimum, the README file) should explain how to install these
dependencies.

Dan

thanks in advance
regards
avi

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