Don't tinker, Reset.

Step-by-step

1. Show Project Navigator
2. Select Project
3. Select Info
4. In Configurations, select each one, one at a time (Debug, ApplicationUnitTest, Release, etc.), and for each target within said configuration, set configuration to None.
5. Make certain that Based on Configuration File reads 0 Configurations Set or No Configurations Set for each configuration. That is the crux.
6. Quit Xcode
7. rm -rf Pods/ Podfile.lock ; pod install

Once you have allowed pod install in step 7 to do its magic, you may be able to use a custom config and change your configurations.

Go into XCode and open your project settings and under the Info tab, you will see "Configurations" where you can set a configuration file for both Debug and Release. You apparently have already set these to some custom config and CocoaPods wants/needs you to use the Pods config.

Ran into the same problem. It would build on the simulator but not on my device. None of the answers solved this for me. Here's what I did piecing some answers together:

1. Changed my pods file to use a specific target:

   target :MyProject do
       pod 'AWSCognitoSync'
       pod 'Facebook-iOS-SDK'
   end
   

2. Ran pod install

3. That gives an error: [!] CocoaPods did not set the base configuration of your project because your project already has a custom config set. In order for CocoaPods integration to work at all, please either set the base configurations of the target `MyProject` to `Pods/Target Support Files/Pods-MyProject/Pods-MyProject.debug.xcconfig` or include the `Pods/Target Support Files/Pods-MyProject/Pods-MyProject.debug.xcconfig` in your build configuration.
4. Go Project settings and click on Info tab. There will be an error where it cannot find the Configuration file. Set it to "None" for Debug and Release.
5. Run pod install yet again
6. Clean and build. This works.

For those coming from the Flutter world, this is a misleading error message suggesting an unnecessary action, and the correct course is to ignore the error and use the flutter cli (not pod), as discussed in https://github.com/flutter/flutter/issues/73845:

gatzsche says a better message would be:

In Flutter pod install should not called manually. To run pod install execute the following commands flutter clean, flutter pub get and flutter build ios.

jmagman notes:

As you point out, the error message is suggesting an action that isn't necessary. The flutter command suppresses that message from pod. You ran pod directly, which isn't a recommended workflow. We don't have any control of error messages coming from CocoaPods, and the flutter command line tool already suppresses the confusing message.

I fixed my issue after a careful reading of the error message:

[!] CocoaPods did not set the base configuration of your project because your project already has a custom config set. In order for CocoaPods integration to work at all, please either set the base configurations of the target Runner to Target Support Files/Pods-Runner/Pods-Runner.profile.xcconfig or include the Target Support Files/Pods-Runner/Pods-Runner.profile.xcconfig in your build configuration (Flutter/Release.xcconfig).

Solution

1. Open Xcode and change the Runner Info Base Configurations to the related Pods-Runner.profile.xconfig.

2. Quit Xcode

3. Terminal: From the ios project folder run pod deintegrate

4. Verify pods are removed

   Project has been deintegrated. No traces of CocoaPods left in project.
   Note: The workspace referencing the Pods project still remains.
   

5. Terminal: From the ios project folder run pod install

(from this original - BAD)

(to this GOOD settings)

Notes

I have not been able to resolve the issue using the second suggestion of including the xconfig file inside of the Flutter/Release.xcconfig configuration file as mentioned in the error message.

You should also make sure that you have no pods in the root of Podfile, you should define all the pods that are used in many targets like that:

def shared_pods
  pod 'ReactiveCocoa', '~> 2.5'
end
target 'app' do
  shared_pods
  pod 'RestKit'
end
target 'tests' do
  shared_pods
  pod 'OCMock'
end

You also might need to delete libPods.a and libPods-app.a from the target dependencies, perform a clean and then run pod install again.

I just ran into this issue after adding some custom build configurations. I could see under:

Pods (target) > Target Support Files > Pods

that it had actually created the new xcconfig files that matched the new build configurations but for some reason I could not select these in the project target of my app.

What fixed it for me was to install and use cocoapods-deintegrate:

gem install cocoapods-deintegrate

and then run:

pod deintegrate

followed by:

pod install

If you added a custom build configuration to your existing project, Cocoapods will complain about it.

Cocoapods will automatically create xcconfig files under the directory Pods/Target Support Files/<build_target> following the naming pattern Pods-<build_target>.<build_config>.xcconfig.

Just make sure to manually add those files to your project in Xcode (under the Pods directory, but not inside the Pods project!). Once those files are included select your project in Xcode, go to the "Info" tab, and expand your custom configuration. Select the appropriate xcconfig file for each target under your custom configuration.

I had the same error while pod install. I tried everything (reinstall pod, update all gems, etc.) and I found solution worked in my case. There was problem because of changing target's name. In this case solution is simple:

1. Click Product -> Scheme -> Manage Schemes...
2. Click on your target on the list and delete it with "-" sign on bottom of window.
3. Click "+" to add target back to list. Choose correct target and name.

After all everything should works.

In case you are using custom config you can follow the suggestion in the warning and include the Pod config in your config file

     #include "Pods/Target Support Files/Pods-YYY/Pods-YYYY.develop-archive.xcconfig"

This will NOT stop the warnings but will allow you to use your private config (there is an open bug on the warning with CocoaPods project) https://github.com/CocoaPods/CocoaPods/issues/2633

The line in the podfile that is generating a problem is : link_with ['BluePlaquesLondon', 'BluePlaquesLondonFramework'].

Just make this : link_with ['BluePlaquesLondon'] or this (worked in my case, hope it will in yours :-)) :

source 'https://github.com/CocoaPods/Specs.git'
platform :ios, '8.0'

xcodeproj 'BluePlaquesLondon.xcodeproj'
inhibit_all_warnings!
link_with ['BluePlaquesLondon']

def import_pods

     pod 'TTTAttributedLabel', '~> 1.10.1'
     pod 'GoogleAnalytics-iOS-SDK', '~> 3.0.9'
     pod 'Google-Maps-iOS-SDK'
     pod 'IntentKit'
     pod 'HCViews'
     pod 'SVProgressHUD', :head
     pod 'iRate'
     pod 'iOS-KML-Framework', :git => 'https://github.com/FLCLjp/iOS-KML-Framework.git'

end

import_pods

target "BluePlaquesLondonFramework" do
    import_pods
    pod 'Kiwi'
end

This is the messages I got after running pod install or pod update:

[!] CocoaPods did not set the base configuration of your project because your project already has a custom config set. In order for CocoaPods integration to work at all, please either set the base configurations of the target `Runner` to `Target Support Files/Pods-Runner/Pods-Runner.debug-staging.xcconfig` or include the `Target Support Files/Pods-Runner/Pods-Runner.debug-staging.xcconfig` in your build configuration (`Flutter/Debug.xcconfig`).

[!] CocoaPods did not set the base configuration of your project because your project already has a custom config set. In order for CocoaPods integration to work at all, please either set the base configurations of the target `Runner` to `Target Support Files/Pods-Runner/Pods-Runner.release-staging.xcconfig` or include the `Target Support Files/Pods-Runner/Pods-Runner.release-staging.xcconfig` in your build configuration (`Flutter/Release.xcconfig`).

[!] CocoaPods did not set the base configuration of your project because your project already has a custom config set. In order for CocoaPods integration to work at all, please either set the base configurations of the target `Runner` to `Target Support Files/Pods-Runner/Pods-Runner.profile-staging.xcconfig` or include the `Target Support Files/Pods-Runner/Pods-Runner.profile-staging.xcconfig` in your build configuration (`Flutter/Release.xcconfig`).

This is what I did to solve the issue:

Add Schemes to Podfile under project 'Runner'

project 'Runner', {
  'Debug' => :debug,
  'Debug-staging' => :debug,
  'Profile' => :release,
  'Profile-staging' => :release,
  'Release' => :release,
  'Release-staging' => :release,
}

Go to ios/Flutter/Debug.xcconfig and include

#include "Pods/Target Support Files/Pods-Runner/Pods-Runner.debug-staging.xcconfig"

Go to ios/Flutter/Release.xcconfig and include

#include "Pods/Target Support Files/Pods-Runner/Pods-Runner.release-staging.xcconfig"
#include "Pods/Target Support Files/Pods-Runner/Pods-Runner.profile-staging.xcconfig"

1. flutter clean
2. Delete podfile.lock
3. Pub get
4. pod install

I moved pods in Podfile outside from the target. File changes from this:

# Uncomment this line to define a global platform for your project
# platform :ios, '8.0'
# Uncomment this line if you're using Swift
use_frameworks!

target 'MyProject' do

pod 'Firebase', '>= 2.5.0'
pod 'Onboard'
pod 'GoogleMaps'
pod 'IQDropDownTextField'

end

To this:

# Uncomment this line to define a global platform for your project
# platform :ios, '8.0'
# Uncomment this line if you're using Swift
use_frameworks!

pod 'Firebase', '>= 2.5.0'
pod 'Onboard'
pod 'GoogleMaps'
pod 'IQDropDownTextField'

target 'MyProject' do

end

Just follow the Android Studio instructions. This is the error output:

"[!] CocoaPods did not set the base configuration of your project because your project already has a custom config set. In order for CocoaPods integration to work at all, please either set the base configurations of the target `Runner` to `Target Support Files/Pods-Runner/Pods-Runner.profile.xcconfig` or include the `Target Support Files/Pods-Runner/Pods-Runner.profile.xcconfig` in your build configuration (`Flutter/Release.xcconfig`)."

In Android Studio IDE go to IOS folder{your project}/ios/Flutter and open the file Release.xxconfig

Then just paste this line:

Target Support Files/Pods-Runner/Pods-Runner.profile.xcconfig

Delete podfile.lock and try to rebuild in Xcode. Worked for me.

1. Add the relevent xcconfig files to your project. Cocoapods will have created them but you can't set them in Xcode until they are in the project.
   • You probably want to add them to the Pods group where the other pods xcconfig files are. Right click and add files.
   • Search for xcconfig files in your project folder or look in Pods/Target Support Files/[TARGET_NAME]/ (I have different cocoapods configured for each target (extension and main project this may be slightly different in your case)
2. Go to project configurations in the Info of your main project
3. For each target and configuration set the appropriate pods configuration.
4. pod install again and you should see no errors.

Sorry my previous answer was unclear. This was just one of many errors i've got while trying to set up Cloud Firestore, so this answer is specific for that situation. In order to solve this error and make firebase work, eventually, you have to follow all of the steps from this page: https://firebase.flutter.dev/docs/firestore/overview/ . If you are having problems with generating the 'firebase_options.dart' file, then you need to follow the steps on this page: https://firebase.google.com/docs/cli#mac-linux-auto-script . The last step is optional, but it reduces build time, and I really don't know how or why, but it made some of other errors also disappear... Step 4. Improve iOS & macOS build times, from this page https://firebase.flutter.dev/docs/firestore/overview/. And off course, don't forget to add dependencies in pubspec.yaml: https://pub.dev/packages/firebase_core/install . There is also a great comment here about using Firebase.initializeApp() : https://stackoverflow.com/a/63492262/17626190

So for me, the problem was due to the aforementioned xcconfig files names being changed before the Swift 3 update took place.

Something was out of sync, so Cocoapods created a 'Recovered References' folder section with the old named files, and linked to them.

To fix this, I:

1. Removed the 'Recovered References' folder and the containing old .xcconfig files from Xcode and file system

2. Quit Xcode

3. Run pod install

Everything was handled for me after then, and the warnings were gone.

I was able to build the project touched by this issue on XCode 6 by:

• selecting Project from the Project Navigator
• choosing Project instead of Target
• going to Info tab
• choosing Pods.(debug/release) Configuration Files from the combobox for the respective Configurations.

Hope this will help someone.

This happened to me because I already had a Pod configuration. I'm new on iOS development, was searching instructions to install Alamofire + SwiftyJSON and ended up installing the libraries more than once, inadvertently. To me, what worked was: on the folder "Target Support Files" in "Pods" project, I selected the two correct .xcconfig files and dragged them to the "Pods" folder of my app project. This enabled the selection of the correct config files on the base configuration.

But then, if I run "pod install" again, the warning will change to the previous .xcconfig file. I try to delete the files and the old framework from the main project but when i ran the previous command once more, gave me the same warning, and created the file "Pods.framework" under the "Pods" folder of my app project. I ignored it, and it seems to be running ok, despite the two frameworks. I don't know if it's right, and a solution, if exists, it would be welcomed.

I had error:

diff: /../Podfile.lock: No such file or directory diff: /Manifest.lock: No such file or directory error: The sandbox is not in sync with the Podfile.lock.

I just checked the path where I was installing the pod and corrected it and installed again,It just worked.

Make sure give the path just before where .xcodeproj or .xcworkspace (if it is already there) exists.

Seems a good ole system restart and probably more importantly it seems I had to reinstall cocoa pods even though the CLI seemed to be in perfectly working condition and had been working for many days before today.

Reinstalled CocoaPods 🤷

sudo gem install cocoapods

It doesn't seem this was the fix for anyone else, but I figured I should post it since this was driving me nuts, and hopefully it helps at least one other person.

After reading the prompt care fully I just open the: Flutter > Release.xconfig After

enter image description here

Before , add another include that they mention in prompt

enter image description here

, Close the Xcode, Run pod deintegrate and pod install , the error gone

I solved this issue by replacing Debug.xcconfig and Release.xcconfig file PRESS cntr + p and search these file and replace all code with

***Debug.xcconfig***
#include "Pods/Target Support Files/Pods-Runner/Pods-Runner.debug.xcconfig"



***Release.xcconfig 
#include "Pods/Target Support Files/Pods-Runner/Pods-Runner.release.xcconfig"
#include "Pods/Target Support Files/Pods-Runner/Pods-Runner.profile.xcconfig"

The simplest solution for this (after having this issue multiple times):

1. Delete Podfile & Podfile.lock from your project library (save Podfile somewhere so you could easily paste to new Podfile)
2. run 'pod init'
3. Edit the 'Podfile' to your will (add pods you are using)
4. run 'pod install'

This would recreate everything and works always in minutes (not spending time to reverse engineer the "bug").