[Bioc-devel] Too many dependencies / MultiAssayExperiment + rtracklayer

Hi all,
Despite moving rarely-used packages to Suggests and eliminating some (e.g.
TCGAutils), the number of dependencies is still listed as 200 for our
package netDx.
https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since
Is there anything else we can do to cut down on dependencies?

Thank you,
Shraddha

On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai<shraddha.pai at utoronto.ca>
wrote:

Hi Michael,
Thanks! Looks like the package trying to load 'rtracklayer' was
'TCGAutils' (see graph from Zugang above, generated using pkgndep - looks
to be quite useful). Turns out TCGAutils really wasn't necessary for my
package so I just took it out and removed all associated dependencies -
mercifully an easier fix.

Thanks for your help,
Shraddha

On Mon, Sep 20, 2021 at 2:57 PM Michael Lawrence <
lawrence.michael at gene.com> wrote:

Hi Shraddha,

 From the rtracklayer perspective, it sounds like Rsamtools is
(indirectly) bringing in those system libraries. I would have expected
zlibbioc to cover the zlib dependency, and perhaps bz2 and lzma
support is optional. Perhaps a core member could comment on that.

In the past, I've used this package
https://github.com/Bioconductor/codetoolsBioC  to identify missing
NAMESPACE imports. In theory, you could remove the rtracklayer import
and run functions in that package to identify the symbol-level
dependencies. The output is a bit noisy though.

Btw, using @importFrom only allows you to be selective of symbol-level
dependencies, not package-level.

Michael

On Mon, Sep 20, 2021 at 11:37 AM Shraddha Pai<shraddha.pai at utoronto.ca>
wrote:

Hello again,
I'm trying to simplify the dependencies for my package "netDx", make it
easier to install. It's currently got over 200(!) + some Unix libraries
that need to be installed.

1. I ran pkgDepMetrics() from BiocPkgTools to find less-needed pkgs, and
the package with the most dependencies is MultiAssayExperiment (see

below

email). I'm using MAE to construct a container - is there a way to use
@importFrom calls to reduce MAE dependencies?

2. Another problem package is rtracklayer which requires Rhtslib, which
requires some unix libraries: zlib1g-dev libbz2-dev liblzma-dev. I'm not
sure which functionality in the package requires rtracklayer - how can I
tell? Is there a way to simplify / reduce these deps so the user doesn't
have to install all these unix packages?

3. Are there other "problem packages" you can see that I can remove?

Let's

assume for now ggplot2 stays because people find it useful to have

plotting

functions readily available.

Thanks very much in advance,
Shraddha
---
"ImportedAndUsed" "Exported" "Usage" "DepOverlap" "DepGainIfExcluded"
"igraph" 1 782 0.13 0.05 0
"ggplot2" 1 520 0.19 0.19 0
"pracma" 1 448 0.22 0.03 0
"plotrix" 1 160 0.62 0.03 1
"S4Vectors" 2 283 0.71 0.03 0
"grDevices" 1 112 0.89 0.01 0
"httr" 1 91 1.1 0.05 0
"scater" 1 85 1.18 0.4 0
"utils" 3 217 1.38 0.01 0
"GenomeInfoDb" 1 60 1.67 0.06 0
"stats" 12 449 2.67 0.01 0
"bigmemory" 1 35 2.86 0.03 3
"RCy3" 12 386 3.11 0.32 18
"BiocFileCache" 1 29 3.45 0.23 3
"glmnet" 1 24 4.17 0.07 2
"parallel" 2 33 6.06 0.01 0
"combinat" 1 13 7.69 0.01 1
"MultiAssayExperiment" 4 46 8.7 0.22 1
"foreach" 2 23 8.7 0.02 0
"graphics" 8 87 9.2 0.01 0
"GenomicRanges" 15 106 14.15 0.08 0
"rappdirs" 1 7 14.29 0.01 0
"reshape2" 1 6 16.67 0.05 0
"RColorBrewer" 1 4 25 0.01 0
"netSmooth" 1 3 33.33 0.82 3
"Rtsne" 1 3 33.33 0.02 0
"doParallel" 1 2 50 0.03 0
"ROCR" 2 3 66.67 0.05 4
"clusterExperiment" NA 122 NA 0.74 0
"IRanges" NA 255 NA 0.04 0


--

*Shraddha Pai, PhD*
Principal Investigator, OICR
Assistant Professor, Department of Molecular Biophysics, University of
Toronto
shraddhapai.com; @spaiglass on Twitter
https://pailab.oicr.on.ca


*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada

M5G

0A3
*@OICR_news*<https://twitter.com/oicr_news>  | *www.oicr.on.ca*
<http://www.oicr.on.ca/>



*Collaborate. Translate. Change lives.*



This message and any attachments may contain confidential and/or

privileged

information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was originally
intended is strictly prohibited. If you have received this message in
error, please contact the sender and delete all copies. Opinions,
conclusions or other information contained in this message may not be

that

of the organization.

--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

	[[alternative HTML version deleted]]

Hi Shraddha,

Note that the badge on the landing page is using this formula (~ from
the `biocViews` package):

```r
db <- available.packages(repos = BiocManager::repositories())
deps <- tools::package_dependencies("netDx", db, recursive = TRUE,
reverse = FALSE, which = "strong")
lengths(deps)
#' netDx
#'??? 109
```

This number is not matching up with the value listed in the badge. Herv?
is currently looking into it
and will have an update soon.

Best regards,

Marcel

On 10/18/21 12:05 PM, Shraddha Pai wrote:

Hi all,
Despite moving rarely-used packages to Suggests and eliminating some (e.g.
TCGAutils), the number of dependencies is still listed as 200 for our
package netDx.
https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since
Is there anything else we can do to cut down on dependencies?

Thank you,
Shraddha

On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai<shraddha.pai at utoronto.ca>
wrote:

Hi Michael,
Thanks! Looks like the package trying to load 'rtracklayer' was
'TCGAutils' (see graph from Zugang above, generated using pkgndep - looks
to be quite useful). Turns out TCGAutils really wasn't necessary for my
package so I just took it out and removed all associated dependencies -
mercifully an easier fix.

Thanks for your help,
Shraddha

On Mon, Sep 20, 2021 at 2:57 PM Michael Lawrence <
lawrence.michael at gene.com> wrote:

Hi Shraddha,

  From the rtracklayer perspective, it sounds like Rsamtools is
(indirectly) bringing in those system libraries. I would have expected
zlibbioc to cover the zlib dependency, and perhaps bz2 and lzma
support is optional. Perhaps a core member could comment on that.

In the past, I've used this package
https://github.com/Bioconductor/codetoolsBioC  to identify missing
NAMESPACE imports. In theory, you could remove the rtracklayer import
and run functions in that package to identify the symbol-level
dependencies. The output is a bit noisy though.

Btw, using @importFrom only allows you to be selective of symbol-level
dependencies, not package-level.

Michael

On Mon, Sep 20, 2021 at 11:37 AM Shraddha Pai<shraddha.pai at utoronto.ca>
wrote:

Hello again,
I'm trying to simplify the dependencies for my package "netDx", make it
easier to install. It's currently got over 200(!) + some Unix libraries
that need to be installed.

1. I ran pkgDepMetrics() from BiocPkgTools to find less-needed pkgs, and
the package with the most dependencies is MultiAssayExperiment (see

below

email). I'm using MAE to construct a container - is there a way to use
@importFrom calls to reduce MAE dependencies?

2. Another problem package is rtracklayer which requires Rhtslib, which
requires some unix libraries: zlib1g-dev libbz2-dev liblzma-dev. I'm not
sure which functionality in the package requires rtracklayer - how can I
tell? Is there a way to simplify / reduce these deps so the user doesn't
have to install all these unix packages?

3. Are there other "problem packages" you can see that I can remove?

Let's

assume for now ggplot2 stays because people find it useful to have

plotting

functions readily available.

Thanks very much in advance,
Shraddha
---
"ImportedAndUsed" "Exported" "Usage" "DepOverlap" "DepGainIfExcluded"
"igraph" 1 782 0.13 0.05 0
"ggplot2" 1 520 0.19 0.19 0
"pracma" 1 448 0.22 0.03 0
"plotrix" 1 160 0.62 0.03 1
"S4Vectors" 2 283 0.71 0.03 0
"grDevices" 1 112 0.89 0.01 0
"httr" 1 91 1.1 0.05 0
"scater" 1 85 1.18 0.4 0
"utils" 3 217 1.38 0.01 0
"GenomeInfoDb" 1 60 1.67 0.06 0
"stats" 12 449 2.67 0.01 0
"bigmemory" 1 35 2.86 0.03 3
"RCy3" 12 386 3.11 0.32 18
"BiocFileCache" 1 29 3.45 0.23 3
"glmnet" 1 24 4.17 0.07 2
"parallel" 2 33 6.06 0.01 0
"combinat" 1 13 7.69 0.01 1
"MultiAssayExperiment" 4 46 8.7 0.22 1
"foreach" 2 23 8.7 0.02 0
"graphics" 8 87 9.2 0.01 0
"GenomicRanges" 15 106 14.15 0.08 0
"rappdirs" 1 7 14.29 0.01 0
"reshape2" 1 6 16.67 0.05 0
"RColorBrewer" 1 4 25 0.01 0
"netSmooth" 1 3 33.33 0.82 3
"Rtsne" 1 3 33.33 0.02 0
"doParallel" 1 2 50 0.03 0
"ROCR" 2 3 66.67 0.05 4
"clusterExperiment" NA 122 NA 0.74 0
"IRanges" NA 255 NA 0.04 0


--

*Shraddha Pai, PhD*
Principal Investigator, OICR
Assistant Professor, Department of Molecular Biophysics, University of
Toronto
shraddhapai.com; @spaiglass on Twitter
https://pailab.oicr.on.ca


*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada

M5G

0A3
*@OICR_news*<https://twitter.com/oicr_news>  | *www.oicr.on.ca*
<http://www.oicr.on.ca/>



*Collaborate. Translate. Change lives.*



This message and any attachments may contain confidential and/or

privileged

information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was originally
intended is strictly prohibited. If you have received this message in
error, please contact the sender and delete all copies. Opinions,
conclusions or other information contained in this message may not be

that

of the organization.

--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

	[[alternative HTML version deleted]]

---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


This email message may contain legally privileged and/or...{{dropped:4}}

Indeed. The wrong set of repos was used for the count:

   db <-
available.packages(repos=BiocManager::repositories(version="3.13"))

   deps <- tools::package_dependencies("netDx", db, recursive=TRUE,
reverse=FALSE, which="strong")

   lengths(deps)

   # netDx

   #   200


Fixed now: https://bioconductor.org/packages/3.14/netDx

Sorry for the inconvenience.

Cheers,
H.


On 18/10/2021 13:31, Marcel Ramos wrote:

Hi Shraddha,

Note that the badge on the landing page is using this formula (~ from
the `biocViews` package):

```r
db <- available.packages(repos = BiocManager::repositories())
deps <- tools::package_dependencies("netDx", db, recursive = TRUE,
reverse = FALSE, which = "strong")
lengths(deps)
#' netDx
#'    109
```

This number is not matching up with the value listed in the badge. Herv?
is currently looking into it
and will have an update soon.

Best regards,

Marcel

On 10/18/21 12:05 PM, Shraddha Pai wrote:

Hi all,
Despite moving rarely-used packages to Suggests and eliminating some

(e.g.

TCGAutils), the number of dependencies is still listed as 200 for our
package netDx.
https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since
Is there anything else we can do to cut down on dependencies?

Thank you,
Shraddha

On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai<shraddha.pai at utoronto.ca>
wrote:

Hi Michael,
Thanks! Looks like the package trying to load 'rtracklayer' was
'TCGAutils' (see graph from Zugang above, generated using pkgndep -

looks

to be quite useful). Turns out TCGAutils really wasn't necessary for my
package so I just took it out and removed all associated dependencies -
mercifully an easier fix.

Thanks for your help,
Shraddha

On Mon, Sep 20, 2021 at 2:57 PM Michael Lawrence <
lawrence.michael at gene.com> wrote:

Hi Shraddha,

  From the rtracklayer perspective, it sounds like Rsamtools is
(indirectly) bringing in those system libraries. I would have expected
zlibbioc to cover the zlib dependency, and perhaps bz2 and lzma
support is optional. Perhaps a core member could comment on that.

In the past, I've used this package
https://github.com/Bioconductor/codetoolsBioC  to identify missing
NAMESPACE imports. In theory, you could remove the rtracklayer import
and run functions in that package to identify the symbol-level
dependencies. The output is a bit noisy though.

Btw, using @importFrom only allows you to be selective of symbol-level
dependencies, not package-level.

Michael

On Mon, Sep 20, 2021 at 11:37 AM Shraddha Pai<

shraddha.pai at utoronto.ca>

wrote:

Hello again,
I'm trying to simplify the dependencies for my package "netDx", make

it

easier to install. It's currently got over 200(!) + some Unix

libraries

that need to be installed.

1. I ran pkgDepMetrics() from BiocPkgTools to find less-needed pkgs,

and

the package with the most dependencies is MultiAssayExperiment (see

below

email). I'm using MAE to construct a container - is there a way to

use

@importFrom calls to reduce MAE dependencies?

2. Another problem package is rtracklayer which requires Rhtslib,

which

requires some unix libraries: zlib1g-dev libbz2-dev liblzma-dev. I'm

not

sure which functionality in the package requires rtracklayer - how

can I

tell? Is there a way to simplify / reduce these deps so the user

doesn't

have to install all these unix packages?

3. Are there other "problem packages" you can see that I can remove?

Let's

assume for now ggplot2 stays because people find it useful to have

plotting

functions readily available.

Thanks very much in advance,
Shraddha
---
"ImportedAndUsed" "Exported" "Usage" "DepOverlap" "DepGainIfExcluded"
"igraph" 1 782 0.13 0.05 0
"ggplot2" 1 520 0.19 0.19 0
"pracma" 1 448 0.22 0.03 0
"plotrix" 1 160 0.62 0.03 1
"S4Vectors" 2 283 0.71 0.03 0
"grDevices" 1 112 0.89 0.01 0
"httr" 1 91 1.1 0.05 0
"scater" 1 85 1.18 0.4 0
"utils" 3 217 1.38 0.01 0
"GenomeInfoDb" 1 60 1.67 0.06 0
"stats" 12 449 2.67 0.01 0
"bigmemory" 1 35 2.86 0.03 3
"RCy3" 12 386 3.11 0.32 18
"BiocFileCache" 1 29 3.45 0.23 3
"glmnet" 1 24 4.17 0.07 2
"parallel" 2 33 6.06 0.01 0
"combinat" 1 13 7.69 0.01 1
"MultiAssayExperiment" 4 46 8.7 0.22 1
"foreach" 2 23 8.7 0.02 0
"graphics" 8 87 9.2 0.01 0
"GenomicRanges" 15 106 14.15 0.08 0
"rappdirs" 1 7 14.29 0.01 0
"reshape2" 1 6 16.67 0.05 0
"RColorBrewer" 1 4 25 0.01 0
"netSmooth" 1 3 33.33 0.82 3
"Rtsne" 1 3 33.33 0.02 0
"doParallel" 1 2 50 0.03 0
"ROCR" 2 3 66.67 0.05 4
"clusterExperiment" NA 122 NA 0.74 0
"IRanges" NA 255 NA 0.04 0


--

*Shraddha Pai, PhD*
Principal Investigator, OICR
Assistant Professor, Department of Molecular Biophysics, University

of

Toronto
shraddhapai.com; @spaiglass on Twitter
https://pailab.oicr.on.ca


*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario,

Canada

M5G

0A3
*@OICR_news*<https://twitter.com/oicr_news>  | *www.oicr.on.ca*
<http://www.oicr.on.ca/>



*Collaborate. Translate. Change lives.*



This message and any attachments may contain confidential and/or

privileged

information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was

originally

intended is strictly prohibited. If you have received this message in
error, please contact the sender and delete all copies. Opinions,
conclusions or other information contained in this message may not be

that

of the organization.

--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical

Computing

Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

     [[alternative HTML version deleted]]

---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


This email message may contain legally privileged and/or...{{dropped:4}}

--
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com

Hi all,
Despite moving rarely-used packages to Suggests and eliminating some (e.g.
TCGAutils), the number of dependencies is still listed as 200 for our
package netDx.
https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since
Is there anything else we can do to cut down on dependencies?

Thank you,
Shraddha

On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai <shraddha.pai at utoronto.ca>
wrote:

Hi Michael,
Thanks! Looks like the package trying to load 'rtracklayer' was
'TCGAutils' (see graph from Zugang above, generated using pkgndep - looks
to be quite useful). Turns out TCGAutils really wasn't necessary for my
package so I just took it out and removed all associated dependencies -
mercifully an easier fix.

Thanks for your help,
Shraddha

On Mon, Sep 20, 2021 at 2:57 PM Michael Lawrence <
lawrence.michael at gene.com> wrote:

Hi Shraddha,

From the rtracklayer perspective, it sounds like Rsamtools is
(indirectly) bringing in those system libraries. I would have expected
zlibbioc to cover the zlib dependency, and perhaps bz2 and lzma
support is optional. Perhaps a core member could comment on that.

In the past, I've used this package
https://github.com/Bioconductor/codetoolsBioC to identify missing
NAMESPACE imports. In theory, you could remove the rtracklayer import
and run functions in that package to identify the symbol-level
dependencies. The output is a bit noisy though.

Btw, using @importFrom only allows you to be selective of symbol-level
dependencies, not package-level.

Michael

On Mon, Sep 20, 2021 at 11:37 AM Shraddha Pai <shraddha.pai at utoronto.ca

wrote:

Hello again,
I'm trying to simplify the dependencies for my package "netDx", make

it

easier to install. It's currently got over 200(!) + some Unix

libraries

that need to be installed.

1. I ran pkgDepMetrics() from BiocPkgTools to find less-needed pkgs,

and

the package with the most dependencies is MultiAssayExperiment (see

below

email). I'm using MAE to construct a container - is there a way to use
@importFrom calls to reduce MAE dependencies?

2. Another problem package is rtracklayer which requires Rhtslib,

which

requires some unix libraries: zlib1g-dev libbz2-dev liblzma-dev. I'm

not

sure which functionality in the package requires rtracklayer - how

can I

tell? Is there a way to simplify / reduce these deps so the user

doesn't

have to install all these unix packages?

3. Are there other "problem packages" you can see that I can remove?

Let's

assume for now ggplot2 stays because people find it useful to have

plotting

functions readily available.

Thanks very much in advance,
Shraddha
---
"ImportedAndUsed" "Exported" "Usage" "DepOverlap" "DepGainIfExcluded"
"igraph" 1 782 0.13 0.05 0
"ggplot2" 1 520 0.19 0.19 0
"pracma" 1 448 0.22 0.03 0
"plotrix" 1 160 0.62 0.03 1
"S4Vectors" 2 283 0.71 0.03 0
"grDevices" 1 112 0.89 0.01 0
"httr" 1 91 1.1 0.05 0
"scater" 1 85 1.18 0.4 0
"utils" 3 217 1.38 0.01 0
"GenomeInfoDb" 1 60 1.67 0.06 0
"stats" 12 449 2.67 0.01 0
"bigmemory" 1 35 2.86 0.03 3
"RCy3" 12 386 3.11 0.32 18
"BiocFileCache" 1 29 3.45 0.23 3
"glmnet" 1 24 4.17 0.07 2
"parallel" 2 33 6.06 0.01 0
"combinat" 1 13 7.69 0.01 1
"MultiAssayExperiment" 4 46 8.7 0.22 1
"foreach" 2 23 8.7 0.02 0
"graphics" 8 87 9.2 0.01 0
"GenomicRanges" 15 106 14.15 0.08 0
"rappdirs" 1 7 14.29 0.01 0
"reshape2" 1 6 16.67 0.05 0
"RColorBrewer" 1 4 25 0.01 0
"netSmooth" 1 3 33.33 0.82 3
"Rtsne" 1 3 33.33 0.02 0
"doParallel" 1 2 50 0.03 0
"ROCR" 2 3 66.67 0.05 4
"clusterExperiment" NA 122 NA 0.74 0
"IRanges" NA 255 NA 0.04 0


--

*Shraddha Pai, PhD*
Principal Investigator, OICR
Assistant Professor, Department of Molecular Biophysics, University of
Toronto
shraddhapai.com; @spaiglass on Twitter
https://pailab.oicr.on.ca


*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario,

Canada

M5G

0A3
*@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
<http://www.oicr.on.ca/>



*Collaborate. Translate. Change lives.*



This message and any attachments may contain confidential and/or

privileged

information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was

originally

intended is strictly prohibited. If you have received this message in
error, please contact the sender and delete all copies. Opinions,
conclusions or other information contained in this message may not be

that

of the organization.

--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

        [[alternative HTML version deleted]]