[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

I'll keep this in mind. Thanks for reminding. Could you please elaborate
your answer on my doubt ? Thanks

On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Please respond on the mailing list, so that others in similar situations
can benefit / contribute.

On 11/11/2016 10:39 AM, Jurat Shayidin wrote:

Dear Martin :

Thanks for your prompt hit . I used to have R release version, so after
I installed devel version of R, I removed R released version, while only
keep devel version instead. Is this correct ? I didn't clean R session,

how can I make it happen on windows?  Plus, How to make R session
vanilla ? What's right configuration both R devel and Bioc devel before

building my packages ? Could you elaborate your answer please? Thank you

very much

Best regards :

On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>

wrote:

    On 11/11/2016 09:44 AM, Jurat Shayidin wrote:

        Dear BiocDevel:

        I ran into the issue after installed devel version of R and Bioc
        3.4.
        Because my packages depends on some packages from CRAN
        repository, now I
        failed to installed paclages from CRAN. I don't have problem
        when I used
        released version of R. Because new packages must coordinate with
        devel
        version of Bioc and R, so I did it. But can't installl packages
        from CRAN
        like dplyr. How can I overcome this issue ? Any quick solution
        ?  I got
        error as follow:


            BiocInstaller::useDevel()

        Error: 'devel' version already in use

            install.packages("dplyr")

        Error in install.packages : missing value where TRUE/FALSE needed


    this does not happen for me; you'll need to debug on your end,
    minimally, reporting the output of traceback() after the error occurs.

    are you in a clean R session with no .RData or other objects loaded
    that might interfere with R?

      R --vanilla

    Martin

    PS -- please do not 'close' questions that have been answered on
    support.bioconductor.org <http://support.bioconductor.org>.





            sessionInfo()

        R Under development (unstable) (2016-11-09 r71642)
        Platform: x86_64-w64-mingw32/x64 (64-bit)
        Running under: Windows >= 8 x64 (build 9200)

        locale:
        [1] LC_COLLATE=English_United States.1252
        [2] LC_CTYPE=English_United States.1252
        [3] LC_MONETARY=English_United States.1252
        [4] LC_NUMERIC=C
        [5] LC_TIME=English_United States.1252

        attached base packages:
        [1] parallel  stats4    stats     graphics  grDevices
        [6] utils     datasets  methods   base

        other attached packages:
         [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
         [3] XVector_0.15.0             rtracklayer_1.35.1
         [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
         [7] IRanges_2.9.7              S4Vectors_0.13.2
         [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2

        loaded via a namespace (and not attached):
         [1] lattice_0.20-34          XML_3.98-1.5
         [3] Rsamtools_1.27.2         Biostrings_2.43.0
         [5] GenomicAlignments_1.11.0 bitops_1.0-6
         [7] grid_3.4.0               zlibbioc_1.21.0
         [9] Matrix_1.2-7.1           BiocParallel_1.9.1
        [11] tools_3.4.0              RCurl_1.95-4.8
        [13] compiler_3.4.0







    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.




--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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.

On 11/11/2016 11:42 AM, Jurat Shayidin wrote:

I'll keep this in mind. Thanks for reminding. Could you please elaborate
your answer on my doubt ? Thanks

On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Please respond on the mailing list, so that others in similar situations

can benefit / contribute.

On 11/11/2016 10:39 AM, Jurat Shayidin wrote:

Dear Martin :

Thanks for your prompt hit . I used to have R release version, so after
I installed devel version of R, I removed R released version, while only
keep devel version instead. Is this correct ? I didn't clean R session,

this is not related to your original question. I personally need both a
release and devel version of R and have both installed.

how can I make it happen on windows?  Plus, How to make R session

vanilla ? What's right configuration both R devel and Bioc devel before

open a Windows shell ('cmd') and type

  R --vanilla

or perhaps

  Rgui --vanilla

building my packages ? Could you elaborate your answer please? Thank you

again, this isn't related to your original question. See the section
'Which version of R?' in

  http://bioconductor.org/developers/how-to/useDevel/

Martin


very much

Best regards :

On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>

wrote:

    On 11/11/2016 09:44 AM, Jurat Shayidin wrote:

        Dear BiocDevel:

        I ran into the issue after installed devel version of R and Bioc
        3.4.
        Because my packages depends on some packages from CRAN
        repository, now I
        failed to installed paclages from CRAN. I don't have problem
        when I used
        released version of R. Because new packages must coordinate with
        devel
        version of Bioc and R, so I did it. But can't installl packages
        from CRAN
        like dplyr. How can I overcome this issue ? Any quick solution
        ?  I got
        error as follow:


            BiocInstaller::useDevel()

        Error: 'devel' version already in use

            install.packages("dplyr")

        Error in install.packages : missing value where TRUE/FALSE
needed


    this does not happen for me; you'll need to debug on your end,
    minimally, reporting the output of traceback() after the error
occurs.

    are you in a clean R session with no .RData or other objects loaded
    that might interfere with R?

      R --vanilla

    Martin

    PS -- please do not 'close' questions that have been answered on
    support.bioconductor.org <http://support.bioconductor.org>.





            sessionInfo()

        R Under development (unstable) (2016-11-09 r71642)
        Platform: x86_64-w64-mingw32/x64 (64-bit)
        Running under: Windows >= 8 x64 (build 9200)

        locale:
        [1] LC_COLLATE=English_United States.1252
        [2] LC_CTYPE=English_United States.1252
        [3] LC_MONETARY=English_United States.1252
        [4] LC_NUMERIC=C
        [5] LC_TIME=English_United States.1252

        attached base packages:
        [1] parallel  stats4    stats     graphics  grDevices
        [6] utils     datasets  methods   base

        other attached packages:
         [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
         [3] XVector_0.15.0             rtracklayer_1.35.1
         [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
         [7] IRanges_2.9.7              S4Vectors_0.13.2
         [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2

        loaded via a namespace (and not attached):
         [1] lattice_0.20-34          XML_3.98-1.5
         [3] Rsamtools_1.27.2         Biostrings_2.43.0
         [5] GenomicAlignments_1.11.0 bitops_1.0-6
         [7] grid_3.4.0               zlibbioc_1.21.0
         [9] Matrix_1.2-7.1           BiocParallel_1.9.1
        [11] tools_3.4.0              RCurl_1.95-4.8
        [13] compiler_3.4.0







    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.




--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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.

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.

sorry for this simple question. why use R vanilla ? not familiar enough
with this term.

On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

On 11/11/2016 11:42 AM, Jurat Shayidin wrote:

I'll keep this in mind. Thanks for reminding. Could you please elaborate
your answer on my doubt ? Thanks

On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Please respond on the mailing list, so that others in similar situations

can benefit / contribute.

On 11/11/2016 10:39 AM, Jurat Shayidin wrote:

Dear Martin :

Thanks for your prompt hit . I used to have R release version, so after
I installed devel version of R, I removed R released version, while only
keep devel version instead. Is this correct ? I didn't clean R session,

this is not related to your original question. I personally need both a
release and devel version of R and have both installed.

how can I make it happen on windows?  Plus, How to make R session

vanilla ? What's right configuration both R devel and Bioc devel before

open a Windows shell ('cmd') and type

  R --vanilla

or perhaps

  Rgui --vanilla

building my packages ? Could you elaborate your answer please? Thank you

again, this isn't related to your original question. See the section
'Which version of R?' in

  http://bioconductor.org/developers/how-to/useDevel/

Martin


very much

Best regards :

On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>

wrote:

    On 11/11/2016 09:44 AM, Jurat Shayidin wrote:

        Dear BiocDevel:

        I ran into the issue after installed devel version of R and Bioc
        3.4.
        Because my packages depends on some packages from CRAN
        repository, now I
        failed to installed paclages from CRAN. I don't have problem
        when I used
        released version of R. Because new packages must coordinate with
        devel
        version of Bioc and R, so I did it. But can't installl packages
        from CRAN
        like dplyr. How can I overcome this issue ? Any quick solution
        ?  I got
        error as follow:


            BiocInstaller::useDevel()

        Error: 'devel' version already in use

            install.packages("dplyr")

        Error in install.packages : missing value where TRUE/FALSE
needed


    this does not happen for me; you'll need to debug on your end,
    minimally, reporting the output of traceback() after the error
occurs.

    are you in a clean R session with no .RData or other objects loaded
    that might interfere with R?

      R --vanilla

    Martin

    PS -- please do not 'close' questions that have been answered on
    support.bioconductor.org <http://support.bioconductor.org>.





            sessionInfo()

        R Under development (unstable) (2016-11-09 r71642)
        Platform: x86_64-w64-mingw32/x64 (64-bit)
        Running under: Windows >= 8 x64 (build 9200)

        locale:
        [1] LC_COLLATE=English_United States.1252
        [2] LC_CTYPE=English_United States.1252
        [3] LC_MONETARY=English_United States.1252
        [4] LC_NUMERIC=C
        [5] LC_TIME=English_United States.1252

        attached base packages:
        [1] parallel  stats4    stats     graphics  grDevices
        [6] utils     datasets  methods   base

        other attached packages:
         [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
         [3] XVector_0.15.0             rtracklayer_1.35.1
         [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
         [7] IRanges_2.9.7              S4Vectors_0.13.2
         [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2

        loaded via a namespace (and not attached):
         [1] lattice_0.20-34          XML_3.98-1.5
         [3] Rsamtools_1.27.2         Biostrings_2.43.0
         [5] GenomicAlignments_1.11.0 bitops_1.0-6
         [7] grid_3.4.0               zlibbioc_1.21.0
         [9] Matrix_1.2-7.1           BiocParallel_1.9.1
        [11] tools_3.4.0              RCurl_1.95-4.8
        [13] compiler_3.4.0







    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.




--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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.

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.

sorry for this simple question. why use R vanilla ? not familiar enough
with this term.

On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

On 11/11/2016 11:42 AM, Jurat Shayidin wrote:

I'll keep this in mind. Thanks for reminding. Could you please elaborate
your answer on my doubt ? Thanks

On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Please respond on the mailing list, so that others in similar situations

can benefit / contribute.

On 11/11/2016 10:39 AM, Jurat Shayidin wrote:

Dear Martin :

Thanks for your prompt hit . I used to have R release version, so

after

I installed devel version of R, I removed R released version, while

only

keep devel version instead. Is this correct ? I didn't clean R

session,

this is not related to your original question. I personally need both a
release and devel version of R and have both installed.

how can I make it happen on windows?  Plus, How to make R session

vanilla ? What's right configuration both R devel and Bioc devel

before

open a Windows shell ('cmd') and type

  R --vanilla

or perhaps

  Rgui --vanilla

building my packages ? Could you elaborate your answer please? Thank you

again, this isn't related to your original question. See the section
'Which version of R?' in

  http://bioconductor.org/developers/how-to/useDevel/

Martin


very much

Best regards :

On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org

wrote:

    On 11/11/2016 09:44 AM, Jurat Shayidin wrote:

        Dear BiocDevel:

        I ran into the issue after installed devel version of R and

Bioc

        3.4.
        Because my packages depends on some packages from CRAN
        repository, now I
        failed to installed paclages from CRAN. I don't have problem
        when I used
        released version of R. Because new packages must coordinate

with

        devel
        version of Bioc and R, so I did it. But can't installl

packages

        from CRAN
        like dplyr. How can I overcome this issue ? Any quick solution
        ?  I got
        error as follow:


            BiocInstaller::useDevel()

        Error: 'devel' version already in use

            install.packages("dplyr")

        Error in install.packages : missing value where TRUE/FALSE
needed


    this does not happen for me; you'll need to debug on your end,
    minimally, reporting the output of traceback() after the error
occurs.

    are you in a clean R session with no .RData or other objects

loaded

    that might interfere with R?

      R --vanilla

    Martin

    PS -- please do not 'close' questions that have been answered on
    support.bioconductor.org <http://support.bioconductor.org>.





            sessionInfo()

        R Under development (unstable) (2016-11-09 r71642)
        Platform: x86_64-w64-mingw32/x64 (64-bit)
        Running under: Windows >= 8 x64 (build 9200)

        locale:
        [1] LC_COLLATE=English_United States.1252
        [2] LC_CTYPE=English_United States.1252
        [3] LC_MONETARY=English_United States.1252
        [4] LC_NUMERIC=C
        [5] LC_TIME=English_United States.1252

        attached base packages:
        [1] parallel  stats4    stats     graphics  grDevices
        [6] utils     datasets  methods   base

        other attached packages:
         [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
         [3] XVector_0.15.0             rtracklayer_1.35.1
         [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
         [7] IRanges_2.9.7              S4Vectors_0.13.2
         [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2

        loaded via a namespace (and not attached):
         [1] lattice_0.20-34          XML_3.98-1.5
         [3] Rsamtools_1.27.2         Biostrings_2.43.0
         [5] GenomicAlignments_1.11.0 bitops_1.0-6
         [7] grid_3.4.0               zlibbioc_1.21.0
         [9] Matrix_1.2-7.1           BiocParallel_1.9.1
        [11] tools_3.4.0              RCurl_1.95-4.8
        [13] compiler_3.4.0







    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.




--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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.

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.

--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

        [[alternative HTML version deleted]]

You're bing asked to use
  R --vanilla
because you have a non-standard problem, exemplified by the fact that what
you have problems with (installing CRAN packages) works for thousands of
users of Bioconductor (certainly for me).  This suggests that there is
something wrong with something on your computer.  Starting R with R
--vanilla disables loading of some user-specific component. If it works
with R --vanilla the conclusion is that whatever made it fail was something
loaded by R but not R --vanilla.  If it doesn't work with R --vanilla the
conclusion is that your problem is elsewhere.

Best,
Kasper

On Fri, Nov 11, 2016 at 12:09 PM, Jurat Shayidin <juratbupt at gmail.com>
wrote:

sorry for this simple question. why use R vanilla ? not familiar enough
with this term.

On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

On 11/11/2016 11:42 AM, Jurat Shayidin wrote:

I'll keep this in mind. Thanks for reminding. Could you please

elaborate

your answer on my doubt ? Thanks

On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Please respond on the mailing list, so that others in similar

situations

can benefit / contribute.

On 11/11/2016 10:39 AM, Jurat Shayidin wrote:

Dear Martin :

Thanks for your prompt hit . I used to have R release version, so

after

I installed devel version of R, I removed R released version, while

only

keep devel version instead. Is this correct ? I didn't clean R

session,

this is not related to your original question. I personally need both a
release and devel version of R and have both installed.

how can I make it happen on windows?  Plus, How to make R session

vanilla ? What's right configuration both R devel and Bioc devel

before

open a Windows shell ('cmd') and type

  R --vanilla

or perhaps

  Rgui --vanilla

building my packages ? Could you elaborate your answer please? Thank you

again, this isn't related to your original question. See the section
'Which version of R?' in

  http://bioconductor.org/developers/how-to/useDevel/

Martin


very much

Best regards :

On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org

wrote:

    On 11/11/2016 09:44 AM, Jurat Shayidin wrote:

        Dear BiocDevel:

        I ran into the issue after installed devel version of R and

Bioc

        3.4.
        Because my packages depends on some packages from CRAN
        repository, now I
        failed to installed paclages from CRAN. I don't have problem
        when I used
        released version of R. Because new packages must coordinate

with

        devel
        version of Bioc and R, so I did it. But can't installl

packages

        from CRAN
        like dplyr. How can I overcome this issue ? Any quick

solution

        ?  I got
        error as follow:


            BiocInstaller::useDevel()

        Error: 'devel' version already in use

            install.packages("dplyr")

        Error in install.packages : missing value where TRUE/FALSE
needed


    this does not happen for me; you'll need to debug on your end,
    minimally, reporting the output of traceback() after the error
occurs.

    are you in a clean R session with no .RData or other objects

loaded

    that might interfere with R?

      R --vanilla

    Martin

    PS -- please do not 'close' questions that have been answered on
    support.bioconductor.org <http://support.bioconductor.org>.





            sessionInfo()

        R Under development (unstable) (2016-11-09 r71642)
        Platform: x86_64-w64-mingw32/x64 (64-bit)
        Running under: Windows >= 8 x64 (build 9200)

        locale:
        [1] LC_COLLATE=English_United States.1252
        [2] LC_CTYPE=English_United States.1252
        [3] LC_MONETARY=English_United States.1252
        [4] LC_NUMERIC=C
        [5] LC_TIME=English_United States.1252

        attached base packages:
        [1] parallel  stats4    stats     graphics  grDevices
        [6] utils     datasets  methods   base

        other attached packages:
         [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
         [3] XVector_0.15.0             rtracklayer_1.35.1
         [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
         [7] IRanges_2.9.7              S4Vectors_0.13.2
         [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2

        loaded via a namespace (and not attached):
         [1] lattice_0.20-34          XML_3.98-1.5
         [3] Rsamtools_1.27.2         Biostrings_2.43.0
         [5] GenomicAlignments_1.11.0 bitops_1.0-6
         [7] grid_3.4.0               zlibbioc_1.21.0
         [9] Matrix_1.2-7.1           BiocParallel_1.9.1
        [11] tools_3.4.0              RCurl_1.95-4.8
        [13] compiler_3.4.0







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