Re: [Bioc-devel] Problem for Biostrings?
Thanks Herve for resolving it. Best, Hai Sent from my iPhone > On 30 Mar 2017, at 06:42, Hervé Pagès <hpa...@fredhutch.org> wrote: > > Hi Hai, > > Looks you added CRAN ggforce recently (in February) to the Suggests > field of Pi. ggforce depends on CRAN package udunits2, which itself > requires system library libudunits2 in order to compile on Linux, > which itself can be installed with > > sudo apt-get install libudunits2-dev > > on Debian/Ubuntu. > > We didn't have libudunits2-dev on malbec2 yet so I just installed it. > The fact that we didn't have it indicates that Pi is the first > Bioconductor package to (indirectly) require it. > > If everything goes as expected, Pi should turn all green on Friday. > > Cheers, > H. > > >> On 03/29/2017 09:08 PM, hfang.shanghai wrote: >> Thanks for the clarification. Now everything is ok except the check in Linux >> (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_malbec2-2Dchecksrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=0Y-86XDQL67bMUlLmRJOg3cEWekH9GHDJNrc5ZEStPg= >> ). The package 'ggforce' is not preinstalled in Linux (others seem fine). >> >> Best, Hai >> >> Sent from my iPhone >> >>> On 29 Mar 2017, at 17:17, Michael Lawrence <lawrence.mich...@gene.com> >>> wrote: >>> >>> It's actually an error in rtracklayer. >>> >>> On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori >>> <lori.sheph...@roswellpark.org> wrote: >>>> That is correct. When the Biostrings package is corrected this ERROR in >>>> your package should resolve automatically. >>>> >>>> >>>> Lori Shepherd >>>> >>>> Bioconductor Core Team >>>> >>>> Roswell Park Cancer Institute >>>> >>>> Department of Biostatistics & Bioinformatics >>>> >>>> Elm & Carlton Streets >>>> >>>> Buffalo, New York 14263 >>>> >>>> >>>> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Hai Fang >>>> <hf...@well.ox.ac.uk> >>>> Sent: Wednesday, March 29, 2017 10:28:39 AM >>>> To: bioc-devel@r-project.org >>>> Subject: [Bioc-devel] Problem for Biostrings? >>>> >>>> Hi, >>>> >>>> I got the error ��object ��inverted�� is not exported by >>>> 'namespace:Biostrings�� at >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=2bhT9aV6mJhSUF8Iq3BZHB_Y2EVt0wNFx6ZcylnnUaE= >>>> . It seems due to the package ��Biostrings�� which failed to pass the >>>> check >>>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Biostrings_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=COIN8OGj-Nd6NzWJEoBq6sXBbJLSqHoZpwPKuGe8DH8= >>>> ). Is it right or something else? >>>> >>>> Thanks, >>>> >>>> Hai >>>> >>>> [[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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=mA0gVnx-5AftDivwP-G_hbeYRiXwDTZj1PW75JbUyeA= >>>> >>>> >>>> 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]] >>>> >>>> >>>> ___
Re: [Bioc-devel] Problem for Biostrings?
Hi Hai, Looks you added CRAN ggforce recently (in February) to the Suggests field of Pi. ggforce depends on CRAN package udunits2, which itself requires system library libudunits2 in order to compile on Linux, which itself can be installed with sudo apt-get install libudunits2-dev on Debian/Ubuntu. We didn't have libudunits2-dev on malbec2 yet so I just installed it. The fact that we didn't have it indicates that Pi is the first Bioconductor package to (indirectly) require it. If everything goes as expected, Pi should turn all green on Friday. Cheers, H. On 03/29/2017 09:08 PM, hfang.shanghai wrote: Thanks for the clarification. Now everything is ok except the check in Linux (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_malbec2-2Dchecksrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=0Y-86XDQL67bMUlLmRJOg3cEWekH9GHDJNrc5ZEStPg= ). The package 'ggforce' is not preinstalled in Linux (others seem fine). Best, Hai Sent from my iPhone On 29 Mar 2017, at 17:17, Michael Lawrence <lawrence.mich...@gene.com> wrote: It's actually an error in rtracklayer. On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: That is correct. When the Biostrings package is corrected this ERROR in your package should resolve automatically. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Hai Fang <hf...@well.ox.ac.uk> Sent: Wednesday, March 29, 2017 10:28:39 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Problem for Biostrings? Hi, I got the error ��object ��inverted�� is not exported by 'namespace:Biostrings�� at https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=2bhT9aV6mJhSUF8Iq3BZHB_Y2EVt0wNFx6ZcylnnUaE= . It seems due to the package ��Biostrings�� which failed to pass the check (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Biostrings_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=COIN8OGj-Nd6NzWJEoBq6sXBbJLSqHoZpwPKuGe8DH8= ). Is it right or something else? Thanks, Hai [[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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=mA0gVnx-5AftDivwP-G_hbeYRiXwDTZj1PW75JbUyeA= 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=mA0gVnx-5AftDivwP-G_hbeYRiXwDTZj1PW75JbUyeA= ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=mA0gVnx-5AftDivwP-G_hbeYRiXwDTZj1PW75JbUyeA= [[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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=mA0gVnx-5AftDivwP-G_hbeYRiXwDTZj1PW75JbUyeA= -- 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 ___ Bioc-devel@
Re: [Bioc-devel] Problem for Biostrings?
Thanks for the clarification. Now everything is ok except the check in Linux (http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/malbec2-checksrc.html). The package 'ggforce' is not preinstalled in Linux (others seem fine). Best, Hai Sent from my iPhone > On 29 Mar 2017, at 17:17, Michael Lawrence <lawrence.mich...@gene.com> wrote: > > It's actually an error in rtracklayer. > > On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori > <lori.sheph...@roswellpark.org> wrote: >> That is correct. When the Biostrings package is corrected this ERROR in >> your package should resolve automatically. >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Cancer Institute >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> >> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Hai Fang >> <hf...@well.ox.ac.uk> >> Sent: Wednesday, March 29, 2017 10:28:39 AM >> To: bioc-devel@r-project.org >> Subject: [Bioc-devel] Problem for Biostrings? >> >> Hi, >> >> I got the error ��object ��inverted�� is not exported by >> 'namespace:Biostrings�� at >> http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/. It seems due to >> the package ��Biostrings�� which failed to pass the check >> (http://bioconductor.org/checkResults/devel/bioc-LATEST/Biostrings/). Is it >> right or something else? >> >> Thanks, >> >> Hai >> >>[[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-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 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem for Biostrings?
It's actually an error in rtracklayer. On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > That is correct. When the Biostrings package is corrected this ERROR in your > package should resolve automatically. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Hai Fang > <hf...@well.ox.ac.uk> > Sent: Wednesday, March 29, 2017 10:28:39 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Problem for Biostrings? > > Hi, > > I got the error “object ‘inverted’ is not exported by 'namespace:Biostrings” > at http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/. It seems due > to the package “Biostrings” which failed to pass the check > (http://bioconductor.org/checkResults/devel/bioc-LATEST/Biostrings/). Is it > right or something else? > > Thanks, > > Hai > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem for Biostrings?
That is correct. When the Biostrings package is corrected this ERROR in your package should resolve automatically. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Hai Fang <hf...@well.ox.ac.uk> Sent: Wednesday, March 29, 2017 10:28:39 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Problem for Biostrings? Hi, I got the error �object �inverted� is not exported by 'namespace:Biostrings� at http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/. It seems due to the package �Biostrings� which failed to pass the check (http://bioconductor.org/checkResults/devel/bioc-LATEST/Biostrings/). Is it right or something else? Thanks, Hai [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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
[Bioc-devel] Problem for Biostrings?
Hi, I got the error “object ‘inverted’ is not exported by 'namespace:Biostrings” at http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/. It seems due to the package “Biostrings” which failed to pass the check (http://bioconductor.org/checkResults/devel/bioc-LATEST/Biostrings/). Is it right or something else? Thanks, Hai [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
