Thanks to both Valerie and Herv� for all the comments with this problem.
Just to let you know, I encountered with this problem while developing the algorithm, initially. In both windows and mac, I wasn't able to run R CMD Check locally due to the same error. In both machines I did a new installation of R and all the packages again and that solved the problem for Mac but not for Windows. Thanks Again! Best, Juan Pablo > but not GenomicFeatures, which is another victim of this > install.packages bug: > > > https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/tokay2-checksrc.html > > AFAICS we've been seeing this problem on tokay2 (Windows) almost every > day for the last few weeks. I guess it started after we updated R to a > more recent R 3.4 on this machine. So I suspect a change in R somehow > triggered this. > > H. > > On 04/15/2017 08:02 PM, Obenchain, Valerie wrote: > EventPointer 0.99.36 built clean today: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=ZxAUJxS48UK2FAs1mcQeAC2XXy0-eiv9SW4OyyOUZDs&e= > > Valerie > On 04/14/2017 09:16 AM, Obenchain, Valerie wrote: >> Hi Juan Pablo, >> >> We think this is a problem related to installed.packages(), see >> discussion here: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DApril_010819.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=bSGL5D0ea0jkhT_HDTBTWVccTXfXi-E7uYm4ZCy4VuY&e= >> >> You can ignore this for now. Thanks for keeping an eye on the build report. >> >> Valerie >> On 04/14/2017 12:41 AM, Romero, Juan Pablo wrote: >>> Hello all, >>> >>> >>> I know that today is the deadline for passing R CMD build and R CMD check >>> without errors and warnings, and my package EventPointer has been working >>> perfectly for the last weeks. >>> >>> >>> Today the build report in tokay2 shows an error in one of the examples: >>> >>> >>> ** running examples for arch 'x64' ... ERROR >>> >>> >>> Make the TxDb object ... Error in if (file.exists(dest) && file.mtime(dest) >>> > file.mtime(lib) && : >>> missing value where TRUE/FALSE needed >>> >>> >>> The error is coming from the function makeTxDbFromGFF and the error does >>> not come from functions from >>> >>> my package. >>> >>> >>> Is anybody having a similar error? >>> >>> >>> I will appreciate any help on this to avoid problems related with adding >>> the package to the new release. >>> >>> >>> Thanks! >>> >>> >>> Best regards, >>> >>> >>> Juan Pablo >>> ________________________________ From: Herv� Pag�s <hpa...@fredhutch.org> Sent: Monday, April 17, 2017 1:51:48 AM To: Obenchain, Valerie; Romero, Juan Pablo; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Error in tokay2 but not GenomicFeatures, which is another victim of this install.packages bug: https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/tokay2-checksrc.html AFAICS we've been seeing this problem on tokay2 (Windows) almost every day for the last few weeks. I guess it started after we updated R to a more recent R 3.4 on this machine. So I suspect a change in R somehow triggered this. H. On 04/15/2017 08:02 PM, Obenchain, Valerie wrote: > EventPointer 0.99.36 built clean today: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=ZxAUJxS48UK2FAs1mcQeAC2XXy0-eiv9SW4OyyOUZDs&e= > > Valerie > > > > On 04/14/2017 09:16 AM, Obenchain, Valerie wrote: >> Hi Juan Pablo, >> >> We think this is a problem related to installed.packages(), see >> discussion here: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DApril_010819.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=bSGL5D0ea0jkhT_HDTBTWVccTXfXi-E7uYm4ZCy4VuY&e= >> >> You can ignore this for now. Thanks for keeping an eye on the build report. >> >> Valerie >> >> >> >> >> On 04/14/2017 12:41 AM, Romero, Juan Pablo wrote: >>> Hello all, >>> >>> >>> I know that today is the deadline for passing R CMD build and R CMD check >>> without errors and warnings, and my package EventPointer has been working >>> perfectly for the last weeks. >>> >>> >>> Today the build report in tokay2 shows an error in one of the examples: >>> >>> >>> ** running examples for arch 'x64' ... ERROR >>> >>> >>> Make the TxDb object ... Error in if (file.exists(dest) && file.mtime(dest) >>> > file.mtime(lib) && : >>> missing value where TRUE/FALSE needed >>> >>> >>> The error is coming from the function makeTxDbFromGFF and the error does >>> not come from functions from >>> >>> my package. >>> >>> >>> Is anybody having a similar error? >>> >>> >>> I will appreciate any help on this to avoid problems related with adding >>> the package to the new release. >>> >>> >>> Thanks! >>> >>> >>> Best regards, >>> >>> >>> Juan Pablo >>> >>> >>> [[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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=Yt38wCbX1caDF2fSTSl4ZafJNM1hanoCXbVbqkFax5M&e= >>> >> >> >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=Yt38wCbX1caDF2fSTSl4ZafJNM1hanoCXbVbqkFax5M&e= >> > > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=Yt38wCbX1caDF2fSTSl4ZafJNM1hanoCXbVbqkFax5M&e= > -- Herv� Pag�s 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 [[alternative HTML version deleted]]
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