Re: [Bioc-devel] BiocCheck error
Hi Marek, Thanks for pointing this out in release. I have applied the patch to BiocCheck version 1.38.1. FWIW, this issue was first opened here https://github.com/Bioconductor/BiocCheck/issues/135 Best regards, Marcel On 1/25/24 9:24 AM, Marek Gierlinski (Staff) wrote: > Yes, it must be this. I�ve installed the devel version and the error is gone. > > Marek > > From: Kern, Lori > Date: Thursday, 25 January 2024 at 14:13 > To: James W. MacDonald , Marek Gierlinski (Staff) > , bioc-devel@r-project.org > > Subject: Re: BiocCheck error > I believe this bug with BiocCheck is fixed in the current devel version > 1.39.21 but will let the contributor that worked on the bug comment for sure. > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > [[alternative HTML version deleted]] > > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Marcel Ramos Pérez Roswell Park Comprehensive Cancer Center Dept. of Biostatistics and Bioinformatics Elm & Carlton Streets Buffalo, New York, 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck error
Yes, it must be this. I�ve installed the devel version and the error is gone. Marek From: Kern, Lori Date: Thursday, 25 January 2024 at 14:13 To: James W. MacDonald , Marek Gierlinski (Staff) , bioc-devel@r-project.org Subject: Re: BiocCheck error I believe this bug with BiocCheck is fixed in the current devel version 1.39.21 but will let the contributor that worked on the bug comment for sure. The University of Dundee is a registered Scottish Charity, No: SC015096 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck error
The mailing list check will only occur accurately on our system. I believe this bug with BiocCheck is fixed in the current devel version 1.39.21 but will let the contributor that worked on the bug comment for sure. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of James W. MacDonald Sent: Thursday, January 25, 2024 9:06 AM To: Marek Gierlinski (Staff) ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocCheck error Are you subscribed to the bioc-devel mailing list? -Original Message- From: Bioc-devel On Behalf Of Marek Gierlinski (Staff) Sent: Thursday, January 25, 2024 5:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocCheck error When running BiocCheck::BiockCheck() on my package, it gets through almost everything and then produces an error: ... * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://secure-web.cisco.com/1PBt7Tc3WJqS1uVmeylyjdT8qmkOP7SJ_zzgyeGL8CquQF6eDI1bCdJBBVw8_qDxtemppEJ1bIX3uTK4gJd0YXvOywJi6qyewfVVRDk4DEFVrV8jCtznrbA0EQdYNISJHLzpurOTdlZkI2zBeE6ReLeR2lIPPXNMnP-9Q-GqW1t0rOAs0d3XWkxN2sjuPaeLfSsAA0HMOyQkfOvxdv-sqh9x6tgLpVQiJ4DXAOdcF1FzYKNx9BFXNwq_d4KNbak02LigDaXd1t_q8ELZqqov7-jjbVZoK_lDOOh95bDJjhV-s09dZVmcJRpVuoAoyi6xa/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__;!!K-Hz7m0Vt54!g8nTl4H3mS0txEb0EhOoiTBpinKkLxt0CndfgUZiq0NZmyclvGxWraoxus7i-EerExUjAEVpD-1753wCHT-xwd190w$ * Checking for support site registration... Maintainer is registered at support site. Error in strsplit(content(response)$watched_tags, split = ",") : non-character argument Is something wrong with my package (it passes Check with no issues)? Or is it a bug? BiocCheck version 1.38.0, Bioconductor 3.18, R 4.3.2, MacOS 14.3. Marek The University of Dundee is a registered Scottish Charity, No: SC015096 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1PBt7Tc3WJqS1uVmeylyjdT8qmkOP7SJ_zzgyeGL8CquQF6eDI1bCdJBBVw8_qDxtemppEJ1bIX3uTK4gJd0YXvOywJi6qyewfVVRDk4DEFVrV8jCtznrbA0EQdYNISJHLzpurOTdlZkI2zBeE6ReLeR2lIPPXNMnP-9Q-GqW1t0rOAs0d3XWkxN2sjuPaeLfSsAA0HMOyQkfOvxdv-sqh9x6tgLpVQiJ4DXAOdcF1FzYKNx9BFXNwq_d4KNbak02LigDaXd1t_q8ELZqqov7-jjbVZoK_lDOOh95bDJjhV-s09dZVmcJRpVuoAoyi6xa/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__;!!K-Hz7m0Vt54!g8nTl4H3mS0txEb0EhOoiTBpinKkLxt0CndfgUZiq0NZmyclvGxWraoxus7i-EerExUjAEVpD-1753wCHT-xwd190w$ ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1ahYxlH9AzUzSK-81JmxdqodguJHB0u5-NMT5JDjBVbhfaLn9OppczhoQtWouPlE14LdklsUyFLK59hoxsNYG9vHgO6AW98DHsvWZHbvygzCa4jbti15vrjIWJN-lRLUvt2zf9DsY80_gyubaATiTpAegzBcfnpOkm1vm1O8BOQHyo5Gqr7IAnF2PiYxFE1Lu5tFyw-cXUlIzEznIs5lMyfwWBW5YkwoVoCsMjA4XvKP8xKKkIwTHf6ncnoQw-Xwn8bMeraJ_tjmT2fbnTJDsDifHc9CaLMprs-vCB9RnohqTqKDoJrHtI2rT55xcUA-z/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck error
Yes, I am. And BiocCheck used to work for me before, suddenly it is crashing with error. Marek From: James W. MacDonald Date: Thursday, 25 January 2024 at 14:07 To: Marek Gierlinski (Staff) , bioc-devel@r-project.org Subject: RE: BiocCheck error Are you subscribed to the bioc-devel mailing list? The University of Dundee is a registered Scottish Charity, No: SC015096 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck error
Are you subscribed to the bioc-devel mailing list? -Original Message- From: Bioc-devel On Behalf Of Marek Gierlinski (Staff) Sent: Thursday, January 25, 2024 5:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocCheck error When running BiocCheck::BiockCheck() on my package, it gets through almost everything and then produces an error: ... * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!g8nTl4H3mS0txEb0EhOoiTBpinKkLxt0CndfgUZiq0NZmyclvGxWraoxus7i-EerExUjAEVpD-1753wCHT-xwd190w$ * Checking for support site registration... Maintainer is registered at support site. Error in strsplit(content(response)$watched_tags, split = ",") : non-character argument Is something wrong with my package (it passes Check with no issues)? Or is it a bug? BiocCheck version 1.38.0, Bioconductor 3.18, R 4.3.2, MacOS 14.3. Marek The University of Dundee is a registered Scottish Charity, No: SC015096 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!g8nTl4H3mS0txEb0EhOoiTBpinKkLxt0CndfgUZiq0NZmyclvGxWraoxus7i-EerExUjAEVpD-1753wCHT-xwd190w$ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocCheck error
When running BiocCheck::BiockCheck() on my package, it gets through almost everything and then produces an error: ... * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... Maintainer is registered at support site. Error in strsplit(content(response)$watched_tags, split = ",") : non-character argument Is something wrong with my package (it passes Check with no issues)? Or is it a bug? BiocCheck version 1.38.0, Bioconductor 3.18, R 4.3.2, MacOS 14.3. Marek The University of Dundee is a registered Scottish Charity, No: SC015096 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck error
Or: you could just rename your NPS repo -> BioTIP and recreate a very simple NPS repo that contains only a README.md file that says: This repository has been moved to https://github.com/xyang2uchicago/BioTIP That kind of redirect should be OK from the grant submission perspective. H. On 8/22/19 04:51, Zhezhen Wang wrote: > I see, thanks Herve and Martin! > Zhezhen > >> On Aug 22, 2019, at 6:00 AM, Martin Morgan wrote: >> >> The requirement that the repository and package name be the same is >> something imposed by Biocondcutor during the submission process (it's >> probably best practice, but that isn't why the requirement is there); once >> the package is accepted it gets cloned into Bioconductor (as BioTIP) the >> github repository used for submission could be deleted -- we will never look >> at the github repository again, the maintainer is responsible for pushing >> changes to the Bioconductor git repository. >> >> So one could create a temporary repository BioTIP and manage the complexity >> of two repositories during submission (basically two remotes 'origin' >> (github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP >> repository, with any changes pushed to both. Once the package is accepted, >> change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete >> github/user/BioTIP. Continue to push to upstream and remote, to keep the >> public github and canonical bioconductor repositories in sync. These steps >> are described at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=dujEzslWeMIvlTaSOpEXKPSBhHSgfjJdT-5vXztzjNc=o36ekG8m2LTVHqFWfa1uu-vxfFxjblw1UE8I7Nm5fpc= >> >> Obviously not ideal, and really a workaround for limitations on the >> Bioconductor side of the fence, but it would not result in two permanent >> github repositories with the same content. >> >> Martin >> >> On 8/22/19, 12:27 AM, "Pages, Herve" wrote: >> >>> On 8/21/19 18:51, Zhezhen Wang wrote: >>> Thank you so much for that remainder. The thing is the NPS linkage is >>> already included in our grant submission, but then we found that there >>> already is a package called NPS so we decided to change it BioTIP. Is >>> making another copy and rename that to BioTIP the best way to solve my >>> situation? >> >> But then isn't it going to be somewhat painful to keep the 2 repos in >> sync? Sounds like using some kind of alias or redirect mechanism would >> be better but you would need to ask the Git or GitHub experts on how to >> do this. >> >> H. >> >>> >>> Zhezhen >>> >>> *From:* Pages, Herve >>> *Sent:* Wednesday, August 21, 2019 7:47 PM >>> *To:* Zhezhen Wang ; Martin Morgan >>> ; Vincent Carey >>> *Cc:* bioc-devel@r-project.org >>> *Subject:* Re: [Bioc-devel] BiocCheck error >>> Note that the name of the package (BioTIP) differs from the name of the >>> GitHub repo (NPS). They will need to match if you intend to submit to >>> Bioconductor. Thanks! >>> >>> H. >>> >>> >>>> On 8/20/19 09:20, Zhezhen Wang wrote: >>>> I see, thank you Martin! >>>> Zhezhen >>>> >>>> From: Martin Morgan >>>> Sent: Tuesday, August 20, 2019 11:15 AM >>>> To: Zhezhen Wang ; Vincent Carey >>>> >>>> Cc: bioc-devel@r-project.org >>>> Subject: Re: [Bioc-devel] BiocCheck error >>>> >>>> I think this is from BiocCheck, needing access to CRAN / Bioconductor to >>>> look at package status. Likely there are issues accessing these sites >>>> (BiocManager::repositories()) from your computer. It seems not to be an >>>> issue that you as developer need to worry about, provided you are >>>> confident that you are using current packages. >>>> >>>> Martin >>>> >>>> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" >>>> wrote: >>>> >>>> The github repo is >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo= >>>&
Re: [Bioc-devel] BiocCheck error
I see, thanks Herve and Martin! Zhezhen > On Aug 22, 2019, at 6:00 AM, Martin Morgan wrote: > > The requirement that the repository and package name be the same is something > imposed by Biocondcutor during the submission process (it's probably best > practice, but that isn't why the requirement is there); once the package is > accepted it gets cloned into Bioconductor (as BioTIP) the github repository > used for submission could be deleted -- we will never look at the github > repository again, the maintainer is responsible for pushing changes to the > Bioconductor git repository. > > So one could create a temporary repository BioTIP and manage the complexity > of two repositories during submission (basically two remotes 'origin' > (github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP > repository, with any changes pushed to both. Once the package is accepted, > change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete > github/user/BioTIP. Continue to push to upstream and remote, to keep the > public github and canonical bioconductor repositories in sync. These steps > are described at http://bioconductor.org/developers/how-to/git/ > > Obviously not ideal, and really a workaround for limitations on the > Bioconductor side of the fence, but it would not result in two permanent > github repositories with the same content. > > Martin > > On 8/22/19, 12:27 AM, "Pages, Herve" wrote: > >>On 8/21/19 18:51, Zhezhen Wang wrote: >> Thank you so much for that remainder. The thing is the NPS linkage is >> already included in our grant submission, but then we found that there >> already is a package called NPS so we decided to change it BioTIP. Is >> making another copy and rename that to BioTIP the best way to solve my >> situation? > >But then isn't it going to be somewhat painful to keep the 2 repos in >sync? Sounds like using some kind of alias or redirect mechanism would >be better but you would need to ask the Git or GitHub experts on how to >do this. > >H. > >> >> Zhezhen >> >> *From:* Pages, Herve >> *Sent:* Wednesday, August 21, 2019 7:47 PM >> *To:* Zhezhen Wang ; Martin Morgan >> ; Vincent Carey >> *Cc:* bioc-devel@r-project.org >> *Subject:* Re: [Bioc-devel] BiocCheck error >> Note that the name of the package (BioTIP) differs from the name of the >> GitHub repo (NPS). They will need to match if you intend to submit to >> Bioconductor. Thanks! >> >> H. >> >> >>> On 8/20/19 09:20, Zhezhen Wang wrote: >>> I see, thank you Martin! >>> Zhezhen >>> >>> From: Martin Morgan >>> Sent: Tuesday, August 20, 2019 11:15 AM >>> To: Zhezhen Wang ; Vincent Carey >>> >>> Cc: bioc-devel@r-project.org >>> Subject: Re: [Bioc-devel] BiocCheck error >>> >>> I think this is from BiocCheck, needing access to CRAN / Bioconductor to >>> look at package status. Likely there are issues accessing these sites >>> (BiocManager::repositories()) from your computer. It seems not to be an >>> issue that you as developer need to worry about, provided you are >>> confident that you are using current packages. >>> >>> Martin >>> >>> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" >>> wrote: >>> >>> The github repo is >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo= >>> >>> >>> >>> From: Vincent Carey >>> Sent: Tuesday, August 20, 2019 10:52 AM >>> To: Zhezhen Wang >>> Cc: bioc-devel@r-project.org >>> Subject: Re: [Bioc-devel] BiocCheck error >>> >>> If your package that generates the error is in a github repo, please >>> give the details. >>> If it is already in Bioconductor please give the name of the package >>> and ensure we can >>> get access to the code that is generating the error. In general it is >>> very hard to help unless >>> we can reproduce the error you report. >>> >>> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang >>> mailto:zhez...@uchicago.edu>> wrote: >>
Re: [Bioc-devel] BiocCheck error
The requirement that the repository and package name be the same is something imposed by Biocondcutor during the submission process (it's probably best practice, but that isn't why the requirement is there); once the package is accepted it gets cloned into Bioconductor (as BioTIP) the github repository used for submission could be deleted -- we will never look at the github repository again, the maintainer is responsible for pushing changes to the Bioconductor git repository. So one could create a temporary repository BioTIP and manage the complexity of two repositories during submission (basically two remotes 'origin' (github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP repository, with any changes pushed to both. Once the package is accepted, change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete github/user/BioTIP. Continue to push to upstream and remote, to keep the public github and canonical bioconductor repositories in sync. These steps are described at http://bioconductor.org/developers/how-to/git/ Obviously not ideal, and really a workaround for limitations on the Bioconductor side of the fence, but it would not result in two permanent github repositories with the same content. Martin On 8/22/19, 12:27 AM, "Pages, Herve" wrote: On 8/21/19 18:51, Zhezhen Wang wrote: > Thank you so much for that remainder. The thing is the NPS linkage is > already included in our grant submission, but then we found that there > already is a package called NPS so we decided to change it BioTIP. Is > making another copy and rename that to BioTIP the best way to solve my > situation? But then isn't it going to be somewhat painful to keep the 2 repos in sync? Sounds like using some kind of alias or redirect mechanism would be better but you would need to ask the Git or GitHub experts on how to do this. H. > > Zhezhen > > *From:* Pages, Herve > *Sent:* Wednesday, August 21, 2019 7:47 PM > *To:* Zhezhen Wang ; Martin Morgan > ; Vincent Carey > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] BiocCheck error > Note that the name of the package (BioTIP) differs from the name of the > GitHub repo (NPS). They will need to match if you intend to submit to > Bioconductor. Thanks! > > H. > > > On 8/20/19 09:20, Zhezhen Wang wrote: >> I see, thank you Martin! >> Zhezhen >> >> From: Martin Morgan >> Sent: Tuesday, August 20, 2019 11:15 AM >> To: Zhezhen Wang ; Vincent Carey >> Cc: bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] BiocCheck error >> >> I think this is from BiocCheck, needing access to CRAN / Bioconductor to look at package status. Likely there are issues accessing these sites (BiocManager::repositories()) from your computer. It seems not to be an issue that you as developer need to worry about, provided you are confident that you are using current packages. >> >> Martin >> >> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" wrote: >> >> The github repo is https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo= >> >> >> ____ >> From: Vincent Carey >> Sent: Tuesday, August 20, 2019 10:52 AM >> To: Zhezhen Wang >> Cc: bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] BiocCheck error >> >> If your package that generates the error is in a github repo, please give the details. >> If it is already in Bioconductor please give the name of the package and ensure we can >> get access to the code that is generating the error. In general it is very hard to help unless >> we can reproduce the error you report. >> >> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang mailto:zhez...@uchicago.edu>> wrote: >> Hi I am running BiocCheck on my new package and I get the following error message >> >>* Checking for deprecated package usage... Warning in readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the connection >> >>
Re: [Bioc-devel] BiocCheck error
On 8/21/19 18:51, Zhezhen Wang wrote:
> Thank you so much for that remainder. The thing is the NPS linkage is
> already included in our grant submission, but then we found that there
> already is a package called NPS so we decided to change it BioTIP. Is
> making another copy and rename that to BioTIP the best way to solve my
> situation?
But then isn't it going to be somewhat painful to keep the 2 repos in
sync? Sounds like using some kind of alias or redirect mechanism would
be better but you would need to ask the Git or GitHub experts on how to
do this.
H.
>
> Zhezhen
>
> *From:* Pages, Herve
> *Sent:* Wednesday, August 21, 2019 7:47 PM
> *To:* Zhezhen Wang ; Martin Morgan
> ; Vincent Carey
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] BiocCheck error
> Note that the name of the package (BioTIP) differs from the name of the
> GitHub repo (NPS). They will need to match if you intend to submit to
> Bioconductor. Thanks!
>
> H.
>
>
> On 8/20/19 09:20, Zhezhen Wang wrote:
>> I see, thank you Martin!
>> Zhezhen
>>
>> From: Martin Morgan
>> Sent: Tuesday, August 20, 2019 11:15 AM
>> To: Zhezhen Wang ; Vincent Carey
>>
>> Cc: bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] BiocCheck error
>>
>> I think this is from BiocCheck, needing access to CRAN / Bioconductor to
>> look at package status. Likely there are issues accessing these sites
>> (BiocManager::repositories()) from your computer. It seems not to be an
>> issue that you as developer need to worry about, provided you are confident
>> that you are using current packages.
>>
>> Martin
>>
>> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang"
>> wrote:
>>
>> The github repo is
>>https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo=
>>
>>
>>
>> From: Vincent Carey
>> Sent: Tuesday, August 20, 2019 10:52 AM
>> To: Zhezhen Wang
>> Cc: bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] BiocCheck error
>>
>> If your package that generates the error is in a github repo, please
>>give the details.
>> If it is already in Bioconductor please give the name of the package
>>and ensure we can
>> get access to the code that is generating the error. In general it is
>>very hard to help unless
>> we can reproduce the error you report.
>>
>> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang
>>mailto:zhez...@uchicago.edu>> wrote:
>> Hi I am running BiocCheck on my new package and I get the following
>>error message
>>
>> * Checking for deprecated package usage... Warning in
>>readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or
>>address could not be resolved' Error in readLines(file, skipNul = TRUE) :
>>cannot open the connection
>>
>> May I know what this error message means and how I can correct it?
>>
>> Zhezhen
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>>
>> The information in this e-mail is intended only for the
>>...{{dropped:14}}
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>>
>>
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Re: [Bioc-devel] BiocCheck error
Thank you so much for that remainder. The thing is the NPS linkage is already
included in our grant submission, but then we found that there already is a
package called NPS so we decided to change it BioTIP. Is making another copy
and rename that to BioTIP the best way to solve my situation?
Zhezhen
From: Pages, Herve
Sent: Wednesday, August 21, 2019 7:47 PM
To: Zhezhen Wang ; Martin Morgan
; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
Note that the name of the package (BioTIP) differs from the name of the
GitHub repo (NPS). They will need to match if you intend to submit to
Bioconductor. Thanks!
H.
On 8/20/19 09:20, Zhezhen Wang wrote:
> I see, thank you Martin!
> Zhezhen
>
> From: Martin Morgan
> Sent: Tuesday, August 20, 2019 11:15 AM
> To: Zhezhen Wang ; Vincent Carey
>
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] BiocCheck error
>
> I think this is from BiocCheck, needing access to CRAN / Bioconductor to look
> at package status. Likely there are issues accessing these sites
> (BiocManager::repositories()) from your computer. It seems not to be an issue
> that you as developer need to worry about, provided you are confident that
> you are using current packages.
>
> Martin
>
> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang"
> wrote:
>
> The github repo is
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo=
>
>
>
> From: Vincent Carey
> Sent: Tuesday, August 20, 2019 10:52 AM
> To: Zhezhen Wang
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] BiocCheck error
>
> If your package that generates the error is in a github repo, please
> give the details.
> If it is already in Bioconductor please give the name of the package and
> ensure we can
> get access to the code that is generating the error. In general it is
> very hard to help unless
> we can reproduce the error you report.
>
> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang
> mailto:zhez...@uchicago.edu>> wrote:
> Hi I am running BiocCheck on my new package and I get the following
> error message
>
>* Checking for deprecated package usage... Warning in
> readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or
> address could not be resolved' Error in readLines(file, skipNul = TRUE) :
> cannot open the connection
>
> May I know what this error message means and how I can correct it?
>
> Zhezhen
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
> The information in this e-mail is intended only for the ...{{dropped:14}}
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] BiocCheck error
Note that the name of the package (BioTIP) differs from the name of the
GitHub repo (NPS). They will need to match if you intend to submit to
Bioconductor. Thanks!
H.
On 8/20/19 09:20, Zhezhen Wang wrote:
> I see, thank you Martin!
> Zhezhen
>
> From: Martin Morgan
> Sent: Tuesday, August 20, 2019 11:15 AM
> To: Zhezhen Wang ; Vincent Carey
>
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] BiocCheck error
>
> I think this is from BiocCheck, needing access to CRAN / Bioconductor to look
> at package status. Likely there are issues accessing these sites
> (BiocManager::repositories()) from your computer. It seems not to be an issue
> that you as developer need to worry about, provided you are confident that
> you are using current packages.
>
> Martin
>
> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang"
> wrote:
>
> The github repo is
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo=
>
>
>
> From: Vincent Carey
> Sent: Tuesday, August 20, 2019 10:52 AM
> To: Zhezhen Wang
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] BiocCheck error
>
> If your package that generates the error is in a github repo, please
> give the details.
> If it is already in Bioconductor please give the name of the package and
> ensure we can
> get access to the code that is generating the error. In general it is
> very hard to help unless
> we can reproduce the error you report.
>
> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang
> mailto:zhez...@uchicago.edu>> wrote:
> Hi I am running BiocCheck on my new package and I get the following
> error message
>
>* Checking for deprecated package usage... Warning in
> readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or
> address could not be resolved' Error in readLines(file, skipNul = TRUE) :
> cannot open the connection
>
> May I know what this error message means and how I can correct it?
>
> Zhezhen
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
> The information in this e-mail is intended only for the ...{{dropped:14}}
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] BiocCheck error
I see, thank you Martin!
Zhezhen
From: Martin Morgan
Sent: Tuesday, August 20, 2019 11:15 AM
To: Zhezhen Wang ; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
I think this is from BiocCheck, needing access to CRAN / Bioconductor to look
at package status. Likely there are issues accessing these sites
(BiocManager::repositories()) from your computer. It seems not to be an issue
that you as developer need to worry about, provided you are confident that you
are using current packages.
Martin
On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang"
wrote:
The github repo is https://github.com/xyang2uchicago/NPS
From: Vincent Carey
Sent: Tuesday, August 20, 2019 10:52 AM
To: Zhezhen Wang
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
If your package that generates the error is in a github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
get access to the code that is generating the error. In general it is very
hard to help unless
we can reproduce the error you report.
On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang
mailto:zhez...@uchicago.edu>> wrote:
Hi I am running BiocCheck on my new package and I get the following error
message
* Checking for deprecated package usage... Warning in readLines(file,
skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not
be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the
connection
May I know what this error message means and how I can correct it?
Zhezhen
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information in this e-mail is intended only for the ...{{dropped:14}}
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Re: [Bioc-devel] BiocCheck error
I think this is from BiocCheck, needing access to CRAN / Bioconductor to look
at package status. Likely there are issues accessing these sites
(BiocManager::repositories()) from your computer. It seems not to be an issue
that you as developer need to worry about, provided you are confident that you
are using current packages.
Martin
On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang"
wrote:
The github repo is https://github.com/xyang2uchicago/NPS
From: Vincent Carey
Sent: Tuesday, August 20, 2019 10:52 AM
To: Zhezhen Wang
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
If your package that generates the error is in a github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
get access to the code that is generating the error. In general it is very
hard to help unless
we can reproduce the error you report.
On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang
mailto:zhez...@uchicago.edu>> wrote:
Hi I am running BiocCheck on my new package and I get the following error
message
* Checking for deprecated package usage... Warning in readLines(file,
skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not
be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the
connection
May I know what this error message means and how I can correct it?
Zhezhen
[[alternative HTML version deleted]]
___
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The information in this e-mail is intended only for the ...{{dropped:14}}
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Re: [Bioc-devel] BiocCheck error
The github repo is https://github.com/xyang2uchicago/NPS
From: Vincent Carey
Sent: Tuesday, August 20, 2019 10:52 AM
To: Zhezhen Wang
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
If your package that generates the error is in a github repo, please give the
details.
If it is already in Bioconductor please give the name of the package and ensure
we can
get access to the code that is generating the error. In general it is very
hard to help unless
we can reproduce the error you report.
On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang
mailto:zhez...@uchicago.edu>> wrote:
Hi I am running BiocCheck on my new package and I get the following error
message
* Checking for deprecated package usage... Warning in readLines(file,
skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not
be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the
connection
May I know what this error message means and how I can correct it?
Zhezhen
[[alternative HTML version deleted]]
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The information in this e-mail is intended only for the ...{{dropped:14}}
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Re: [Bioc-devel] BiocCheck error
If your package that generates the error is in a github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
get access to the code that is generating the error. In general it is very
hard to help unless
we can reproduce the error you report.
On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang wrote:
> Hi I am running BiocCheck on my new package and I get the following error
> message
>
> * Checking for deprecated package usage... Warning in readLines(file,
> skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could
> not be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the
> connection
>
> May I know what this error message means and how I can correct it?
>
> Zhezhen
>
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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[Bioc-devel] BiocCheck error
Hi I am running BiocCheck on my new package and I get the following error message * Checking for deprecated package usage... Warning in readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the connection May I know what this error message means and how I can correct it? Zhezhen [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck error
Martin,
Thank you. yes, you are right.
Now it works, I also changed outputs to tempfile() or tempdir().
Aimin
On Tue, Apr 10, 2018 at 6:07 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> Hi Aimin -- the problem is that your vignette has two VignetteEngine
> commands in it
>
> PathwaySplice/vignettes master$ grep VignetteEngine *
> tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown}
> tutorial.Rmd: %\VignetteEngine{knitr::knitr}
>
> Also, please avoid writing to files in the user system, replace 'C:/temp'
> with tempfile() or dir = tempfile(); dir.create(dir) in code like the
> following
>
> PathwaySplice master$ grep -r "C:/" *
> man/runPathwaySplice.Rd: output.file='C:/temp/test.csv')
> man/runPathwaySplice.Rd: output.file='C:/temp/test.csv')
> man/enrichmentMap.Rd: label.node.by.index = TRUE,
> output.file.dir='C:/temp')
> man/enrichmentMap.Rd: label.node.by.index = FALSE,
> output.file.dir='C:/temp')}
> man/compareResults.Rd:compareResults(20, res.adj, res.unadj,
> gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
> R/Run_pathwaysplice.R:#' output.file='C:/temp/test.csv')
> R/Run_pathwaysplice.R:#' output.file='C:/temp/test.csv')
> R/Run_pathwaysplice.R:#' label.node.by.index = TRUE,
> output.file.dir='C:/temp')
> R/Run_pathwaysplice.R:#' label.node.by.index =
> FALSE, output.file.dir='C:/temp')}
> R/Run_pathwaysplice.R:#' compareResults(20, res.adj, res.unadj,
> gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
>
> Martin
>
>
> On 04/10/2018 04:39 PM, Aimin Yan wrote:
>
>> I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed
>> without errors and warnings.
>>
>> However I get the following error when I use "R CMD BiocCheck
>> PathwaySplice_1.3.0.tar.gz"
>>
>> R CMD BiocCheck PathwaySplice_1.3.0.tar.gz
>>
>> This is BiocCheck version 1.15.8. BiocCheck is a work in progress.
>>
>> Output and severity of issues may change. Installing package...
>>
>> * Checking for version number mismatch...
>>
>> * Checking if other packages can import this one...
>>
>> * Checking to see if we understand object initialization...
>>
>> * NOTE: Consider clarifying how 12 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)
>>
>>winMenuAddItem (.onAttach)
>>
>>ggplot (compareResults2)
>>
>>aes (compareResults2)
>>
>>random_sampling_200k (compareResults2)
>>
>>PValue (compareResults2)
>>
>>PathwaySplice (compareResults2)
>>
>>geom_point (compareResults2)
>>
>>geom_smooth (compareResults2)
>>
>>labs (compareResults2)
>>
>>scale_colour_manual (compareResults2)
>>
>>scale_shape_manual (compareResults2)
>>
>>get.col.scale (netplot)
>>
>> * Checking vignette directory...
>>
>> This is a software package
>>
>> Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) :
>>
>>values must be length 1,
>>
>> but FUN(X[[1]]) result is length 2
>>
>> Calls: ... BiocCheck -> checkVignetteDir -> checkVigBuilder ->
>> vapply
>>
>> Execution halted
>>
>>
>>
>> Any idea about this?
>>
>>
>> Here is my sessionInfo()
>>
>> https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4
>>
>> Thank you,
>>
>> Aimin
>>
>> [[alternative HTML version deleted]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
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Re: [Bioc-devel] BiocCheck error
Hi Aimin -- the problem is that your vignette has two VignetteEngine
commands in it
PathwaySplice/vignettes master$ grep VignetteEngine *
tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown}
tutorial.Rmd: %\VignetteEngine{knitr::knitr}
Also, please avoid writing to files in the user system, replace
'C:/temp' with tempfile() or dir = tempfile(); dir.create(dir) in code
like the following
PathwaySplice master$ grep -r "C:/" *
man/runPathwaySplice.Rd:
output.file='C:/temp/test.csv')
man/runPathwaySplice.Rd:
output.file='C:/temp/test.csv')
man/enrichmentMap.Rd: label.node.by.index = TRUE,
output.file.dir='C:/temp')
man/enrichmentMap.Rd: label.node.by.index = FALSE,
output.file.dir='C:/temp')}
man/compareResults.Rd:compareResults(20, res.adj, res.unadj,
gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
R/Run_pathwaysplice.R:#'
output.file='C:/temp/test.csv')
R/Run_pathwaysplice.R:#'
output.file='C:/temp/test.csv')
R/Run_pathwaysplice.R:#' label.node.by.index =
TRUE, output.file.dir='C:/temp')
R/Run_pathwaysplice.R:#' label.node.by.index =
FALSE, output.file.dir='C:/temp')}
R/Run_pathwaysplice.R:#' compareResults(20, res.adj, res.unadj,
gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
Martin
On 04/10/2018 04:39 PM, Aimin Yan wrote:
I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed
without errors and warnings.
However I get the following error when I use "R CMD BiocCheck
PathwaySplice_1.3.0.tar.gz"
R CMD BiocCheck PathwaySplice_1.3.0.tar.gz
This is BiocCheck version 1.15.8. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking for version number mismatch...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 12 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)
winMenuAddItem (.onAttach)
ggplot (compareResults2)
aes (compareResults2)
random_sampling_200k (compareResults2)
PValue (compareResults2)
PathwaySplice (compareResults2)
geom_point (compareResults2)
geom_smooth (compareResults2)
labs (compareResults2)
scale_colour_manual (compareResults2)
scale_shape_manual (compareResults2)
get.col.scale (netplot)
* Checking vignette directory...
This is a software package
Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) :
values must be length 1,
but FUN(X[[1]]) result is length 2
Calls: ... BiocCheck -> checkVignetteDir -> checkVigBuilder ->
vapply
Execution halted
Any idea about this?
Here is my sessionInfo()
https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4
Thank you,
Aimin
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[Bioc-devel] BiocCheck error
I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed without errors and warnings. However I get the following error when I use "R CMD BiocCheck PathwaySplice_1.3.0.tar.gz" R CMD BiocCheck PathwaySplice_1.3.0.tar.gz This is BiocCheck version 1.15.8. BiocCheck is a work in progress. Output and severity of issues may change. Installing package... * Checking for version number mismatch... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 12 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) winMenuAddItem (.onAttach) ggplot (compareResults2) aes (compareResults2) random_sampling_200k (compareResults2) PValue (compareResults2) PathwaySplice (compareResults2) geom_point (compareResults2) geom_smooth (compareResults2) labs (compareResults2) scale_colour_manual (compareResults2) scale_shape_manual (compareResults2) get.col.scale (netplot) * Checking vignette directory... This is a software package Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) : values must be length 1, but FUN(X[[1]]) result is length 2 Calls: ... BiocCheck -> checkVignetteDir -> checkVigBuilder -> vapply Execution halted Any idea about this? Here is my sessionInfo() https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4 Thank you, Aimin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocCheck Error 'duplicate label install'?
Greetings, Apologies if this is a double post, I was over zealous in my initial submission that I didn't wait for my membership to be confirmed. I have 'finished' creating a package I would like to submit to bioconductor. As per the instructions on the bioconductor website I am trying to get the package to pass the BiocCheck function but I keep getting the following error: Error in parse_block(g[-1], g[1], params.src) : duplicate label 'install' The package also passes through R CMD Check with no errors or warnings. If someone could kindly explain what this error means I would sincerely appreciate it. Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck Error 'duplicate label install'?
- Original Message - From: Charles Determan Jr deter...@umn.edu To: bioc-devel@r-project.org Sent: Wednesday, December 31, 2014 11:41:09 AM Subject: [Bioc-devel] BiocCheck Error 'duplicate label install'? Greetings, Apologies if this is a double post, I was over zealous in my initial submission that I didn't wait for my membership to be confirmed. I have 'finished' creating a package I would like to submit to bioconductor. As per the instructions on the bioconductor website I am trying to get the package to pass the BiocCheck function but I keep getting the following error: Error in parse_block(g[-1], g[1], params.src) : duplicate label 'install' It could be a bug in BiocCheck. Can you send me your package off-list? Then I'll be able to reproduce the problem and figure out what's going on. Thanks, Dan The package also passes through R CMD Check with no errors or warnings. If someone could kindly explain what this error means I would sincerely appreciate it. Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
