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Improve consistency among message, warnings, and errors #28

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Improve consistency among message, warnings, and errors #28

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Now message() is uniformly used instead of cat(), warning() is used
for warnings instead of cat(), correct spacing is added between
arguments where appropriate, and error messages do not have trailing
newlines, since stop() already adds one.

m.carlson and others added 30 commits October 15, 2011 00:36
adds sva to the repos.
cfb92b0 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59266 bc3139a8-67e5-0310-9ffc-ced21a209358
adds sva to the repos.
a317a90 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59266 bc3139a8-67e5-0310-9ffc-ced21a209358
(1) Added ComBat to sva, (2) updated vignette with ComBat section, (3…
7c494aa 
…) added man files for ComBat

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59673 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
(1) Added ComBat to sva, (2) updated vignette with ComBat section, (3…
da6747b 
…) added man files for ComBat

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59673 bc3139a8-67e5-0310-9ffc-ced21a209358
added ComBat.Rd
f2f4695 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59716 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
added ComBat.Rd
20643fb 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59716 bc3139a8-67e5-0310-9ffc-ced21a209358
removed svadat.Rd
e5c4290 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59717 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
removed svadat.Rd
e7e3376 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59717 bc3139a8-67e5-0310-9ffc-ced21a209358
bumped package version numbers prior to creating 2.9 branch
b89d11a 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
@dtenenba
bumped package version numbers prior to creating 2.9 branch
1f3ee88 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
version bump for start of 2.10 development cycle
3738a21 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
@dtenenba
version bump for start of 2.10 development cycle
593a122 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
Set default method to be for num svs in sva package. Gave users optio…
eaedd7f 
…n of setting num.sv method in sva. Fixed a bug in Combat so only an intercept term can be included

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@60980 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
Set default method to be for num svs in sva package. Gave users optio…
f8293bb 
…n of setting num.sv method in sva. Fixed a bug in Combat so only an intercept term can be included

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@60980 bc3139a8-67e5-0310-9ffc-ced21a209358
Fixed num.sv documentation to put method be first, updated vignette t…
1e2fb24 
…o use method leek

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@61130 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
Fixed num.sv documentation to put method be first, updated vignette t…
50eb0a4 
…o use method leek

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@61130 bc3139a8-67e5-0310-9ffc-ced21a209358
Fixed Combat bug so that numerical covariates can appear anywhere in …
1106d60 
…the list, updated fsva to include the new fast method as well as the original method

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@63723 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
Fixed Combat bug so that numerical covariates can appear anywhere in …
1289e85 
…the list, updated fsva to include the new fast method as well as the original method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@63723 bc3139a8-67e5-0310-9ffc-ced21a209358
first version bump prior to creating 2.10 branch
af42e2c 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
@dtenenba
first version bump prior to creating 2.10 branch
ee27ffe 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
bumped version numbers after creating 2.10 branch
cec4dfa 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
@dtenenba
bumped version numbers after creating 2.10 branch
8437d97 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
fixed bug in the sweave document that was preventing windows binary f…
9e855b7 
…rom being built. removed bug in fsva where svs where being normalized incorrectly for the exact case.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@65411 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
fixed bug in the sweave document that was preventing windows binary f…
725b3c0 
…rom being built. removed bug in fsva where svs where being normalized incorrectly for the exact case.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@65411 bc3139a8-67e5-0310-9ffc-ced21a209358
update Imports:
8b52703 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@69763 bc3139a8-67e5-0310-9ffc-ced21a209358
update Imports:
3d8f2a0 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@69763 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump all packages before creating 2.11 branch.
302e04a 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
@dtenenba
Bump all packages before creating 2.11 branch.
f048950 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
bump package versions after creating 2.11 branch
3c51864 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
@dtenenba
bump package versions after creating 2.11 branch
ff3a47c 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
hpages@fhcrc.org and others added 18 commits April 24, 2017 19:25
bump x.y.z versions to even y prior to creation of 3_5 branch
27b8bd2 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
bump x.y.z versions to even y prior to creation of 3_5 branch
1af467f 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
bump x.y.z versions to odd y after creation of 3_5 branch
a3406ad 
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
bump x.y.z versions to odd y after creation of 3_5 branch
812b539 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
@jtleek
Merge pull request jtleek#26 from cafletezbrant/master
7e4aa44 
Fixed the bug from a month ago
Resolved branch conflicts
d1ed1ca 
From: Leonardo Collado Torres <lcollado@jhsph.edu>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130117 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
Resolved branch conflicts
21b0a7f 
From: Leonardo Collado Torres <lcollado@jhsph.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130117 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
v3.25.1 -- merged https://github.com/jtleek/sva-devel with svn's history
5cbe819
@lcolladotor
v3.25.1 -- merged https://github.com/jtleek/sva-devel with svn's history
4622dd0 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130118 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
Fix my email
a46c42f
@lcolladotor
Fix my email
d749131 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130119 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
v3.25.2 -- resolve some notes/errors/warnings from R CMD check
acc1784
@lcolladotor
v3.25.2 -- resolve some notes/errors/warnings from R CMD check
c5444ca 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130304 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
v3.25.3 -- fixed another error and a note
411e91b
@lcolladotor
v3.25.3 -- fixed another error and a note
076e768 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130416 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
v3.25.4 -- fixed a namespace warning
9d75a30
@lcolladotor
v3.25.4 -- fixed a namespace warning
a7fd565 
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130528 bc3139a8-67e5-0310-9ffc-ced21a209358
@lcolladotor
Merge remote-tracking branch 'upstream/master'
9ef4627
@DarwinAwardWinner
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Note that message and warning send the output to stderr, as opposed to cat, which sends to stdout, so this slightly more than a simple cosmetic code change.

This was referenced Sep 7, 2017
Closed
Closed
kasperdanielhansen and others added 6 commits October 6, 2017 09:07
@kasperdanielhansen
Update ComBat.R
842412c 
Changed two occurences of `cat()` to `message()` in ComBat so they can be suppressed. All the other printing in ComBat already uses `message()`.
@jtleek
Merge pull request jtleek#32 from kasperdanielhansen/patch-2
ce5bb6b 
Update ComBat.R
@hpages
bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
3cc5e75
@hpages
bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
7e929b7
@lcolladotor
Merge remote-tracking branch 'upstream/master'
e1d30f4
@DarwinAwardWinner
Improve consistency among message, warnings, and errors
8ca4fb9 
Now message() is uniformly used instead of cat(), warning() is used
for warnings instead of cat(), correct spacing is added between
arguments where appropriate, and error messages do not have trailing
newlines, since stop() already adds one.
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@DarwinAwardWinner @jtleek @dtenenba @sonali-bioc @lcolladotor @kasperdanielhansen @hpages