Apktool: brut.androlib.AndrolibException: brut.common.BrutException: could not exec (exit code = 1)

Information

1. Apktool version: v2.4.0-3cf5cb-SNAPSHOT
2. OS: Linux kali 4.18.0-kali3-amd64 #1 SMP Debian 4.18.20-2kali2 (2018-11-30) x86_64 GNU/Linux
3. Source: Google Play Store

Issue description

Apktool fails to re-build LinkedIn from the Play Store.

Affected packages

• com.linkedin.android - https://play.google.com/store/apps/details?id=com.linkedin.android

Example

[root:/tmp/manual-run]# apktool d -o com.linkedin.android.decompiled com.linkedin.android.apk 
I: Using Apktool 2.4.0-3cf5cb-SNAPSHOT on com.linkedin.android.apk
I: Loading resource table...
I: Decoding AndroidManifest.xml with resources...
I: Loading resource table from file: /root/.local/share/apktool/framework/1.apk
I: Regular manifest package...
I: Decoding file-resources...
I: Decoding values */* XMLs...
I: Baksmaling classes.dex...
I: Baksmaling classes2.dex...
I: Baksmaling classes3.dex...
I: Baksmaling classes4.dex...
I: Baksmaling classes5.dex...
I: Baksmaling classes6.dex...
I: Baksmaling classes7.dex...
I: Baksmaling classes8.dex...
I: Copying assets and libs...
I: Copying unknown files...
I: Copying original files...
[root:/tmp/manual-run]# apktool b -o nochanges.apk com.linkedin.android.decompiled 
I: Using Apktool 2.4.0-3cf5cb-SNAPSHOT
I: Checking whether sources has changed...
I: Smaling smali folder into classes.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes2 folder into classes2.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes7 folder into classes7.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes8 folder into classes8.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes5 folder into classes5.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes3 folder into classes3.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes6 folder into classes6.dex...
I: Checking whether sources has changed...
I: Smaling smali_classes4 folder into classes4.dex...
I: Checking whether resources has changed...
I: Building resources...
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:102: error: Public symbol array/company_bar_chart_colors declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:103: error: Public symbol array/contact_sync_type_all_or_no_keys declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:104: error: Public symbol array/contact_sync_type_all_or_no_values declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:105: error: Public symbol array/contact_sync_type_keys declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:106: error: Public symbol array/contact_sync_type_values declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:107: error: Public symbol array/degree_bar_chart_colors declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:108: error: Public symbol array/entities_max_commute_time declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:109: error: Public symbol array/entities_premium_function_colors declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:110: error: Public symbol array/growth_join_email_list declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:111: error: Public symbol array/linked_out_disruption_type declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:112: error: Public symbol array/linked_out_request_method declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:113: error: Public symbol array/live_bar_chart_colors declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:114: error: Public symbol array/month_array declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:115: error: Public symbol array/notification_channel declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:116: error: Public symbol array/rest_li_request_method declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:117: error: Public symbol array/search_alert_frequency declared here is not defined.
W: /tmp/manual-run/com.linkedin.android.decompiled/res/values/public.xml:118: error: Public symbol array/skill_bar_chart_colors declared here is not defined.
brut.androlib.AndrolibException: brut.common.BrutException: could not exec (exit code = 1): [/tmp/brut_util_Jar_3175894518026574016.tmp, p, --forced-package-id, 127, --min-sdk-version, 21, --target-sdk-version, 28, --version-code, 116400, --version-name, 4.1.256, --no-version-vectors, -F, /tmp/APKTOOL6202122347419265887.tmp, -0, arsc, -0, META-INF/android.support.design_material.version, -0, META-INF/androidx.appcompat_appcompat.version, -0, META-INF/androidx.arch.core_core-runtime.version, -0, META-INF/androidx.asynclayoutinflater_asynclayoutinflater.version, -0, META-INF/androidx.browser_browser.version, -0, META-INF/androidx.cardview_cardview.version, -0, META-INF/androidx.coordinatorlayout_coordinatorlayout.version, -0, META-INF/androidx.core_core.version, -0, META-INF/androidx.cursoradapter_cursoradapter.version, -0, META-INF/androidx.customview_customview.version, -0, META-INF/androidx.databinding_baseAdapters.version, -0, META-INF/androidx.databinding_library.version, -0, META-INF/androidx.documentfile_documentfile.version, -0, META-INF/androidx.drawerlayout_drawerlayout.version, -0, META-INF/androidx.dynamicanimation_dynamicanimation.version, -0, META-INF/androidx.exifinterface_exifinterface.version, -0, META-INF/androidx.fragment_fragment.version, -0, META-INF/androidx.interpolator_interpolator.version, -0, META-INF/androidx.legacy_legacy-support-core-ui.version, -0, META-INF/androidx.legacy_legacy-support-core-utils.version, -0, META-INF/androidx.legacy_legacy-support-v4.version, -0, META-INF/androidx.lifecycle_lifecycle-extensions.version, -0, META-INF/androidx.lifecycle_lifecycle-livedata-core.version, -0, META-INF/androidx.lifecycle_lifecycle-livedata.version, -0, META-INF/androidx.lifecycle_lifecycle-process.version, -0, META-INF/androidx.lifecycle_lifecycle-runtime.version, -0, META-INF/androidx.lifecycle_lifecycle-service.version, -0, META-INF/androidx.lifecycle_lifecycle-viewmodel.version, -0, META-INF/androidx.loader_loader.version, -0, META-INF/androidx.localbroadcastmanager_localbroadcastmanager.version, -0, META-INF/androidx.media_media.version, -0, META-INF/androidx.preference_preference.version, -0, META-INF/androidx.print_print.version, -0, META-INF/androidx.recyclerview_recyclerview.version, -0, META-INF/androidx.slidingpanelayout_slidingpanelayout.version, -0, META-INF/androidx.swiperefreshlayout_swiperefreshlayout.version, -0, META-INF/androidx.transition_transition.version, -0, META-INF/androidx.vectordrawable_vectordrawable-animated.version, -0, META-INF/androidx.vectordrawable_vectordrawable.version, -0, META-INF/androidx.versionedparcelable_versionedparcelable.version, -0, META-INF/androidx.viewpager_viewpager.version, -0, META-INF/com.google.android.material_material.version, -0, png, -0, webp, -0, arsc, -I, /root/.local/share/apktool/framework/1.apk, -S, /tmp/manual-run/com.linkedin.android.decompiled/res, -M, /tmp/manual-run/com.linkedin.android.decompiled/AndroidManifest.xml]

Steps to Reproduce

1. apktool d <APK>
2. apktool b <folder>

Extra information

1. I have tried apktool d, apktool b without changing anything;
2. I cloned the repo and built from source;
3. The issue goes away if I use the -r flag - which is not useful since I want to modify the resources (namely AndroidManifest.xml).