cran resubmission fix lic. specification

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2021-08-08.
-Once it is accepted, delete this file and tag the release (commit 6c3da7fd2b).
+This package was submitted to CRAN on 2021-08-19.
+Once it is accepted, delete this file and tag the release (commit 768691f534).

LICENSE

@@ -1,12 +1,45 @@
-
 YEAR:2021
 COPYRIGHT HOLDER: NA
 ORGANIZATION: National Institute of Allergy and Infectious Diseases (NIAID), a participating institute of the National Institutes of Health (NIH)
 
+Copyright (c) 2021, COPYRIGHT HOLDER: NA
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+    Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+
+    Neither the name of the <ORGANIZATION> nor the names of its
+    contributors may be used to endorse or promote products derived
+    from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE
+
+
+=======================================
+ALTERNATIVE LICENSE INFORMATION FOLLOWS
+=======================================
+
 R package dsb (all versions)
 • DEFINITIONS: AUTHOR(S) Matthew Mulè, Andrew Martins, John Tsang
 • PROVIDER: The National Institute of Allergy and Infectious Diseases (NIAID), a participating institute of the National Institutes of Health (NIH), and an agency of the United States Government.
-• SOFTWARE: the human readable source code form, the machine readable, binary, object code form, and the related documentation for the modules of the dsb_0.1.0 software package, which is an R package for normalizing single cell data.
+• SOFTWARE: the human readable source code form, the machine readable, binary, object code form, and the related documentation for the modules of the dsb software package, which is an R package for normalizing single cell data.
 • RECIPIENT: the party that downloads the software.
 By downloading or otherwise receiving the SOFTWARE, RECIPIENT may use and/or redistribute the
 SOFTWARE, with or without modification, subject to RECIPIENT’s agreement to the following terms:

R/zzz.r

@@ -1,9 +1,9 @@
 dsbmessage <- function()
 {
   mesg <-
-    cat("dsb package for CITE-seq protein normalization loaded \n",
-        "please cite our paper (under review) at: https://www.biorxiv.org/content/10.1101/2020.02.24.963603v1 \n",
-        "see vignette at https://github.com/niaid/dsb"
+    cat("dsb package for ADT normalization loaded \n",
+        "please cite our paper (under review) at: https://www.biorxiv.org/content/10.1101/2020.02.24.963603v3 \n",
+        "questions: https://github.com/niaid/dsb Vignette: https://cran.r-project.org/package=dsb"
     )
   return(mesg)
 }

cran-comments.md

@@ -1,62 +1,28 @@
-## Submission Aug 9 2021 
+## Submission Aug 26 2021 
 
-This is a resubmission -- please read correspondence about license below. I have specified the license as instructed by the CRAN team from my last CRAN release; *the license is unchanged from the last release*. 
+This is a resubmission:  
 
-Re License components with restrictions and base license permitting such: "Please only ship the CRAN template for the BSD_3_claus license." SEE BELOW.
+In response to: 
 
     ########################### 
-    On 1/24/21, 7:55 PM, "Mule, Matthew (NIH/NIAID) [F]" <matthew.mule AT nih.gov> wrote:
+    Tnanks, I think your LICENSE file is not clear:
 
-    1) re: "Please only ship the CRAN template for the BSD_3_clause license."
-
-    Following instructions sent via email 9 Jan, 2021 below to add the CRAN template for BSD-3 which I have added "in addition to the
-    alternate BSD text" as written below. Please do let me know if I misunderstood? 
-       
-    On 1/9/21, 8:53 AM, "Uwe Ligges" <ligges AT statistik.tu-dortmund.de> wrote:
-
-    I understood now, but then you need:
+    I'd suggest to start with the BSD_3_clause template.
+    Afterwards perhaps add a well recognizable separator (as other team 
+    members have not udnerstood this is about an extra license) and say an 
+    alternative license follows as in:
 
-    License: BSD_3_clause + file LICENSE | file LICENSE
 
-    and you need in file LICENSE the CRAN template for the BSD_3_clause licene and in addition the alterative BSD text that is
-    currently listed there anyway.
+    =======================================
+    ALTERNATIVE LICENSE INFORMATION FOLLOWS
+    =======================================
 
     ###########################
 
-## Submission Aug 7 2021 
-
-Update submission for version 0.2.0
-
-1 NOTE - I (creator / maintainor) changed my email address from: <matthew.mule at nih.gov> to: <mattmule at gmail.com> The latter is a stable long term email address, the former email address is not consistently accessible and will be invalid after 2023. 
-
-## R CMD check results
-devtools::check(args = c('--as-cran'))  
-0 errors ✓ | 0 warnings ✓ | 0 notes ✓
-
-## Test environments
-* Winbuilder
-  devtools::check_win_release()
- * x86_64-w64-mingw32 (64-bit)
-
-* devtools::check_rhub(pkg = ".")  
-PLEASE NOTE [Bioconductor does not yet build and check packages for R version 4.2](https://github.com/r-hub/rhub/issues/471)
-  * Windows Server 2008 R2 SP1, R-devel, 32/64 bit (see note above) 
-  * Ubuntu Linux 16.04 LTS, R-release, GCC
-  * Fedora Linux, R-devel, clang, gfortran
+I have added the template for the BSD3 clause license as well as the additional limited liability text which is required for software developed by the US National Institutes of Health, separated by the suggested separator: 
 
-re: custom license used in this package; this is the same license as in CRAN v0.1.0 Please refer to Cran team comments from 2021/01/24. Following instructions sent via email 9 Jan, 2021, the CRAN template for BSD-3 is listed "in addition to the alternate BSD text". License documents are referenced in the description as instructed (see email below on specification of license file).
-
-   ########################### 
-   On 1/9/21, 8:53 AM, "Uwe Ligges" <ligges<AT>statistik.tu-dortmund.de> wrote:
-
-       I understood now, but then you need:
-
-       License: BSD_3_clause + file LICENSE | file LICENSE
-
-       and you need in file LICENSE the CRAN template for the BSD_3_clause 
-       licene and in addition the alterative BSD text that is currently listed 
-       there anyway.
-   ###########################
-
-
-
+    =======================================
+    ALTERNATIVE LICENSE INFORMATION FOLLOWS
+    =======================================
+
+    R package dsb... [remainder of additional license text]

inst/CITATION

@@ -0,0 +1,16 @@
+citHeader("To cite dsb in publications use:")
+
+citEntry(
+  entry    = "Article",
+  author   = personList(as.person("Matthew P. Mulè"),
+                        as.person("Andrew J. Martins"),
+                        as.person("John S. Tsang")),
+  title    = "Normalizing and denoising protein expression data from droplet-based single cell profiling",
+  journal  = "Biorxiv",
+  year     = 2021,
+  doi = "10.1101/2020.02.24.963603",
+  url      = "https://www.biorxiv.org/content/10.1101/2020.02.24.963603v3",
+  textVersion = paste(
+  "Mulè and Martins et al. Normalizing and denoising protein expression data from droplet-based single cell profiling. Biorxiv (2021) [dsb]"
+  )
+)